Impacts to Water Quality and Fish Habitat Associated with Maintaining Natural Channels for Flood Control

A field investigation conducted on Boulder Creek in Boulder, Colorado evaluated impacts of flood control maintenance activities on flood conveyance, water quality, and fish habitat. Thirty-nine transects were monitored at one control site and two maintenance sites over a period of eight months. Each site was visited on more than 50 occasions in order to characterize pre- and post-maintenance conditions, and to monitor maintenance activities. Measurements along the transects included substrate composition, flow depth, velocity, and elevation. Reach-average values were assigned to variables such as in-stream vegetation, streambank stability, and woody vegetation before and after maintenance. Water temperature, dissolved oxygen, pH, specific conductance, and turbidity were sampled, and habitat suitability indices were developed pre- and post-maintenance for seven indicator fish species. Water quality impacts during maintenance consisted of high turbidity levels (> 400 NTU), which returned to background levels (0.1–15 NTU) overnight, as well as changes in mean temperature and pH. Alteration of physical channel characteristics as a result of maintenance had limited effects on habitat quality for four of seven fish species, but caused improvements in habitat quality for three fish species. The main implications of this study for floodplain management are that: (1) Flood control maintenance practices can be in direct conflict with water quality and fish habitat objectives, and should be carefully designed and implemented by an interdisciplinary team. (2) Physical habitat for some fish species can be improved as well as reduced by maintenance activities. Habitat suitability curves may be useful tools for evaluating limiting factors of the habitat and for identifying opportunities for habitat improvements as part of maintenance.     

Reduced complexity models for regional aquatic habitat suitability assessment

Generalizable methods that identify suitable aquatic habitat across large river basins and regions are needed to inform resource management. Habitat suitability models intersect environmental variables to predict species occurrence, but are often data intensive and thus are typically developed at small spatial scales. This study estimated mean monthly aquatic habitat suitability throughout Utah (USA) for Bonneville Cutthroat Trout (Oncorhynchus clarkii utah) and Bluehead Sucker (Catostomus discobolus) with publicly available, geospatial datasets. We evaluated 15 habitat suitability models using unique combinations of percent of mean annual discharge, velocity, gradient, and stream temperature. Environmental variables were validated with observed conditions and species presence observations to verify habitat suitability estimates. Stream temperature, gradient, and discharge best predicted Bonneville Cutthroat Trout presence, and gradient and discharge best predicted Bluehead Sucker presence. Simple aquatic habitat suitability models outperformed models that used only streamflow to estimate habitat for both species, and are useful for conservation planning and water resources decision-making. This modeling approach could enable resource managers to prioritize stream restoration across vast regions within their management domain, and is potentially compatible with water management modeling to improve ecological objectives in management models.     

Linkages Between Nutrients and Assemblages of Macroinvertebrates and Fish in Wadeable Streams: Implication to Nutrient Criteria Development

We sampled 240 wadeable streams across Wisconsin for different forms of phosphorus and nitrogen, and assemblages of macroinvertebrates and fish to (1) examine how macroinvertebrate and fish measures correlated with the nutrients; (2) quantify relationships between key biological measures and nutrient forms to identify potential threshold levels of nutrients to support nutrient criteria development; and (3) evaluate the importance of nutrients in influencing biological assemblages relative to other physicochemical factors at different spatial scales. Twenty-three of the 35 fish and 18 of the 26 macroinvertebrate measures significantly correlated (P < 0.05) with at least one nutrient measure. Percentages of carnivorous, intolerant, and omnivorous fishes, index of biotic integrity, and salmonid abundance were fish measures correlated with the most nutrient measures and had the highest correlation coefficients. Percentages of Ephemeroptera–Plecoptera–Trichoptera individuals and taxa, Hilsenhoff biotic index, and mean tolerance value were macroinvertebrate measures that most strongly correlated with the most nutrient measures. Selected biological measures showed clear trends toward degradation as concentrations of phosphorus and nitrogen increased, and some measures showed clear thresholds where biological measures changed drastically with small changes in nutrient concentrations. Our selected environmental factors explained 54% of the variation in the fish assemblages. Of this explained variance, 46% was attributed to catchment and instream habitat, 15% to nutrients, 3% to other water quality measures, and 36% to the interactions among all the environmental variables. Selected environmental factors explained 53% of the variation in macroinvertebrate assemblages. Of this explained variance, 42% was attributed to catchment and instream habitat, 22% to nutrients, 5% to other water quality measures, and 32% to the interactions among all the environmental variables.     

Selenium Bioaccumulation in Stocked Fish as an Indicator of Fishery Potential in Pit Lakes on Reclaimed Coal Mines in Alberta, Canada

Pit lakes are a common reclamation strategy for open pit mines; however, there is a concern about their water quality and suitability as fish habitat because they are often contaminated by metals or metalloids. This study assessed the exposure of fish and invertebrates to selenium (Se) and other metals and metalloids in pit lakes formed by open pit coal mining in Tertiary (thermal coal) and in Cretaceous (metallurgical coal) bedrock. Juvenile hatchery rainbow trout, Oncorhynchus mykiss, and brook trout, Salvelinus fontinalis, were stocked into two thermal coal pit lakes (water Se < 2 μg/L, low water Se) and two metallurgical coal pit lakes (water Se > 15 μg/L, high water Se). Se accumulation in stocked fish and concentrations in invertebrates were characterized over a period of 2 years. In the metallurgical pits, invertebrates had higher Se concentrations and fish accumulated Se to higher levels (exceeding USEPA tissue Se guidelines) than biota in the thermal pits. Rainbow and brook trout accumulated similar concentrations of Se in their muscle and exhibited a similar relationship between whole-body and muscle Se concentrations. These results may be used by resource managers to assess compliance with whole-body tissue Se guidelines and to determine if pit lakes in coal mining areas pose a significant Se risk to wildlife or human health. The high Se exposure in metallurgical coal pits indicates that under the current mining and reclamation strategy, these lakes are not suitable for management as recreational “put and take” fisheries.     

Delineation and Validation of River Network Spatial Scales for Water Resources and Fisheries Management

Identifying appropriate spatial scales is critically important for assessing health, attributing data, and guiding management actions for rivers. We describe a process for identifying a three-level hierarchy of spatial scales for Michigan rivers. Additionally, we conduct a variance decomposition of fish occurrence, abundance, and assemblage metric data to evaluate how much observed variability can be explained by the three spatial scales as a gage of their utility for water resources and fisheries management. The process involved the development of geographic information system programs, statistical models, modification by experienced biologists, and simplification to meet the needs of policy makers. Altogether, 28,889 reaches, 6,198 multiple-reach segments, and 11 segment classes were identified from Michigan river networks. The segment scale explained the greatest amount of variation in fish abundance and occurrence, followed by segment class, and reach. Segment scale also explained the greatest amount of variation in 13 of the 19 analyzed fish assemblage metrics, with segment class explaining the greatest amount of variation in the other six fish metrics. Segments appear to be a useful spatial scale/unit for measuring and synthesizing information for managing rivers and streams. Additionally, segment classes provide a useful typology for summarizing the numerous segments into a few categories. Reaches are the foundation for the identification of segments and segment classes and thus are integral elements of the overall spatial scale hierarchy despite reaches not explaining significant variation in fish assemblage data.     

EFFECTS OF MULTI‐SCALE ENVIRONMENTAL CHARACTERISTICS ON AGRICULTURAL STREAM BIOTA IN EASTERN WISCONSIN1

ABSTRACT: The U.S. Geological Survey examined 25 agricultural streams in eastern Wisconsin the determine relations between fish, invertebrate, and algal metrics and multiple spatial scales of land cover, geologic setting, hydrologic, aquatic habitat, and water chemistry data. Spearman correlation and redundancy analyses were used to examine relations among biotic metrics and environmental characteristics. Riparian vegetation, geologic, and hydrologic conditions affected the response of biotic metrics to watershed agricultural land cover but the relations were aquatic assemblage dependent. It was difficult to separate the interrelated effects of geologic setting, watershed and buffer land cover, and base flow. Watershed and buffer land cover, geologic setting, reach riparian vegetation width, and stream size affected the fish IBI, invertebrate diversity, diatom IBI, and number of algal taxa; however, the invertebrate FBI, percentage of EPT, and the diatom pollution index were more influenced by nutrient concentrations and flow variability. Fish IBI scores seemed most sensitive to land cover in the entire stream network buffer, more so than watershed‐scale land cover and segment or reach riparian vegetation width. All but one stream with more than approximately 10 percent buffer agriculture had fish IBI scores of fair or poor. In general, the invertebrate and algal metrics used in this study were not as sensitive to land cover effects as fish metrics. Some of the reach‐scale characteristics, such as width/depth ratios, velocity, and bank stability, could be related to watershed influences of both land cover and geologic setting. The Wisconsin habitat index was related to watershed geologic setting, watershed and buffer land cover, riparian vegetation width, and base flow, and appeared to be a good indicator of stream quality Results from this study emphasize the value of using more than one or two biotic metrics to assess water quality and the importance of environmental characteristics at multiple scales.     

Testing a GIS Model of Habitat Suitability for a Declining Grassland Bird

Demand for information that can be used to manage loggerhead shrikes has recently increased because of concern over declining populations and loss of open, non-forested habitat. A previously-developed habitat model was modified to predict shrike habitat quality on Fort Riley Military Reservation (FRMR) in Kansas. Shrike habitat suitability indices were calculated based on the amount of potential and usable foraging habitat, and the number of potential nesting sites within a specified area. Interpretation of high quality digital photographs was used to delineate land cover classes, hedgerows and tree counts. These data were entered into a geographic information system (GIS) as individual data sets. The shrike habitat model was then employed to produce a GIS database predicting low, moderate, and high quality shrike habitat throughout the Reservation. Model results indicated that 67% of the Reservation was suitable habitat for loggerhead shrikes. Although over 80% of FRMR was mapped as grassland, the presence of few to several isolated trees or hedgerows was identified as a key factor in modeling habitat suitability. The accuracy of the GIS model was 82% in predicting suitable (moderate and high quality) loggerhead shrike habitat using an independent set of 66 recent shrike observations. The number of potential nesting sites and percent cover of usable foraging habitat were significantly related to habitat suitability of the sites occupied by shrikes.     

Effects of Impervious Cover at Multiple Spatial Scales on Coastal Watershed Streams1

Abstract: The spatial scale and location of land whose development has the strongest influence on aquatic ecosystems must be known to support land use decisions that protect water resources in urbanizing watersheds. We explored impacts of urbanization on streams in the West River watershed, New Haven, Connecticut, to identify the spatial scale of watershed imperviousness that was most strongly related to water chemistry, macroinvertebrates, and physical habitat. A multiparameter water quality index was used to characterize regional urban nonpoint source pollution levels. We identified a critical level of 5% impervious cover, above which stream health declined. Conditions declined with increasing imperviousness and leveled off in a constant state of impairment at 10%. Instream variables were most correlated (0.77 ≤ |r| ≤ 0.92, p < 0.0125) to total impervious area (TIA) in the 100‐m buffer of local contributing areas (～5‐km² drainage area immediately upstream of each study site). Water and habitat quality had a relatively consistent strong relationship with TIA across each of the spatial scales of investigation, whereas macroinvertebrate metrics produced noticeably weaker relationships at the larger scales. Our findings illustrate the need for multiscale watershed management of aquatic ecosystems in small streams flowing through the spatial hierarchies that comprise watersheds with forest‐urban land use gradients.     

Multivariate Condition Assessment of Watersheds with Linked Micromaps

A challenge for statewide stream monitoring is visualizing the spatial and statistical characteristics of such data to compare the biotic condition of watersheds and relate that condition to watershed‐level estimates of instream variables. We used linked micromaps on stream survey data of 25 subbasins (766‐5,982 km²) for biotic condition, nine water quality, and two habitat variables. Subbasin biotic condition was negatively correlated with conductivity, magnesium and sulfate concentrations, and weakly positively correlated with habitat scores of sedimentation and embeddedness, with higher scores indicating better habitat. Positive spatial autocorrelation was detected among the subbasins in both habitat variables, iron concentration, pH, and exceedances of fecal coliform criteria as shown in linked micromaps. A spatial principal components analysis reduced the 11 environmental variables to two principal axes. The first axis synthesized a gradient of water quality and habitat scores among the subbasins. Subbasin biotic condition regressed on first axis subbasin scores had a significant, negative slope and accounted for 55% of the variation. Subbasins in degraded biotic condition had elevated conductivities and ion concentrations in northern and southern subbasins, and low habitat scores in western subbasins. Through linked micromaps, we compared the biotic condition among subbasins and identified stressors prevalent among subbasins that affected biotic condition.     

Prioritizing Stream Barrier Removal to Maximize Connected Aquatic Habitat and Minimize Water Scarcity

Instream barriers, such as dams, culverts, and diversions, alter hydrologic processes and aquatic habitat. Removing uneconomical and aging instream barriers is increasingly used for river restoration. Historically, selection of barrier removal projects used score‐and‐rank techniques, ignoring cumulative change and the spatial structure of stream networks. Likewise, most water supply models prioritize either human water uses or aquatic habitat, failing to incorporate both human and environmental water use benefits. Here, a dual‐objective optimization model identifies barriers to remove that maximize connected aquatic habitat and minimize water scarcity. Aquatic habitat is measured using monthly average streamflow, temperature, channel gradient, and geomorphic condition as indicators of aquatic habitat suitability. Water scarcity costs are minimized using economic penalty functions while a budget constraint specifies the money available to remove barriers. We demonstrate the approach using a case study in Utah's Weber Basin to prioritize removal of instream barriers for Bonneville cutthroat trout, while maintaining human water uses. Removing 54 instream barriers reconnects about 160 km of quality‐weighted habitat and costs approximately US$10 M. After this point, the cost‐effectiveness of removing barriers to connect river habitat decreases. The modeling approach expands barrier removal optimization methods by explicitly including both economic and environmental water uses.     

The Role of Periphyton in Mediating the Effects of Pollution in a Stream Ecosystem

The effects of pollutants on primary producers ramify through ecosystems because primary producers provide food and structure for higher trophic levels and they mediate the biogeochemical cycling of nutrients and contaminants. Periphyton (attached algae) were studied as part of a long-term biological monitoring program designed to guide remediation efforts by the Department of Energy’s Y-12 National Security Complex on East Fork Poplar Creek (EFPC) in Oak Ridge, Tennessee. High concentrations of nutrients entering EFPC were responsible for elevated periphyton production and placed the stream in a state of eutrophy. High rates of primary production at upstream locations in EFPC were associated with alterations in both invertebrate and fish communities. Grazers represented >50% of the biomass of invertebrates and fish near the Y-12 Complex but <10% at downstream and reference sites. An index of epilithic periphyton production accounted for 95% of the site-to-site variation in biomass of grazing fish. Analyses of heavy metals in EFPC periphyton showed that concentrations of zinc, cadmium, copper and nickel in periphyton decreased exponentially with distance downstream from Y-12. Zinc uptake by periphyton was estimated to reduce the concentration of this metal in stream water ~60% over a 5-km reach of EFPC. Management options for mitigating eutrophy in EFPC include additional reductions in nutrient inputs and/or allowing streamside trees to grow and shade the stream. However, reducing periphyton growth may lead to greater downstream transport of contaminants while simultaneously causing higher concentrations of mercury and PCBs in fish at upstream sites.     

Quantifying Florida Bay Habitat Suitability for Fishes and Invertebrates Under Climate Change Scenarios

The Florida Bay ecosystem supports a number of economically important ecosystem services, including several recreational fisheries, which may be affected by changing salinity and temperature due to climate change. In this paper, we use a combination of physical models and habitat suitability index models to quantify the effects of potential climate change scenarios on a variety of juvenile fish and lobster species in Florida Bay. The climate scenarios include alterations in sea level, evaporation and precipitation rates, coastal runoff, and water temperature. We find that the changes in habitat suitability vary in both magnitude and direction across the scenarios and species, but are on average small. Only one of the seven species we investigate (Lagodon rhomboides, i.e., pinfish) sees a sizable decrease in optimal habitat under any of the scenarios. This suggests that the estuarine fauna of Florida Bay may not be as vulnerable to climate change as other components of the ecosystem, such as those in the marine/terrestrial ecotone. However, these models are relatively simplistic, looking only at single species effects of physical drivers without considering the many interspecific interactions that may play a key role in the adjustment of the ecosystem as a whole. More complex models that capture the mechanistic links between physics and biology, as well as the complex dynamics of the estuarine food web, may be necessary to further understand the potential effects of climate change on the Florida Bay ecosystem.     

A method to create simplified versions of existing habitat suitability index (HSI) models

The habitat evaluation procedures (HEP), developed by the US Fish and Wildlife Service, are widely used in the United States to determine the impacts of major construction projects on fish and wildlife habitats. HEP relies heavily on habitat suitability index (HSI) models that use measurements of important habitat characteristics to rate habitat quality for a species on a scale of 0 (unsuitable) to 1.0 (optimal). This report describes a method to simplify existing HSI models to reduce the time and expense involved in sampling habitat variables. Simplified models for three species produced HSI values within 0.2 of those predicted by the original models 90% of the time. Simplified models are particularly useful for rapid habitat inventories and evaluations, wildlife management, and impact assessments in extensive areas or with limited time and personnel.     

Spatial-Scale Effects on Relative Importance of Physical Habitat Predictors of Stream Health

A common theme in recent landscape studies is the comparison of riparian and watershed land use as predictors of stream health. The objective of this study was to compare the performance of reach-scale habitat and remotely assessed watershed-scale habitat as predictors of stream health over varying spatial extents. Stream health was measured with scores on a fish index of biotic integrity (IBI) using data from 95 stream reaches in the Eastern Corn Belt Plain (ECBP) ecoregion of Indiana. Watersheds hierarchically nested within the ecoregion were used to regroup sampling locations to represent varying spatial extents. Reach habitat was represented by metrics of a qualitative habitat evaluation index, whereas watershed variables were represented by riparian forest, geomorphology, and hydrologic indices. The importance of reach- versus watershed-scale variables was measured by multiple regression model adjusted-R² and best subset comparisons in the general linear statistical framework. Watershed models had adjusted-R² ranging from 0.25 to 0.93 and reach models had adjusted-R² ranging from 0.09 to 0.86. Better-fitting models were associated with smaller spatial extents. Watershed models explained about 15% more variation in IBI scores than reach models on average. Variety of surficial geology contributed to decline in model predictive power. Results should be interpreted bearing in mind that reach habitat was qualitatively measured and only fish assemblages were used to measure stream health. Riparian forest and length-slope (LS) factor were the most important watershed-scale variables and mostly positively correlated with IBI scores, whereas substrate and riffle-pool quality were the important reach-scale variables in the ECBP.     

TEMPORAL VARIABILITY OF WATER QUALITY IN THE ST. LUCIE ESTUARY,SOUTH FLORIDA1

ABSTRACT: Four years of monthly freshwater discharge and constituent concentration data from three tributaries were related to a concurrent series of data for three segments of the St. Lucie Estuary in South Florida using multiple regression and time-series analysis techniques. Water quality parameters examined were dissolved inorganic and total nitrogen and phosphorus, chlorophyll a, total suspended solids, turbidity, and color. On monthly time scales, a multiple regression, which included freshwater discharge, freshwater constituent concentration, and dilution with ocean water (salinity) as independent variables, explained 50 percent or less of the variability in estuarine constituents. No single independent variable explained more variation than another. By contrast, on seasonal (wet, dry) time scales, freshwater discharge explained the bulk of variation in estuarine water quality (up to 93 percent). On monthly time scales, variability in concentrations of nutrients and other constituents may be largely controlled by processes internal to the system. At seasonal time scales, freshwater discharge appears to drive variability in most estuarine water quality parameters examined. Results indicate that management of tributary input on a seasonal basis, with the expectation of achieving seasonal concentration goals in the estuary, would have a higher probability of success than managing on a monthly basis.     

EFFECTS OF WATERSHED BEST MANAGEMENT PRACTICES ON HABITAT AND FISH IN WISCONSIN STREAMS1

ABSTRACT: We evaluated the effectiveness of watershed‐scale implementations of best‐management practices (BMPs) for improving habitat and fish attributes in two coldwater stream systems in Wisconsin. We sampled physical habitat, water temperature, and fish communities in multiple paired treatment and reference streams before and after upland (barnyard runoff controls, manure storage, contour plowing, reduced tillage) and riparian (stream bank fencing, sloping, limited rip‐rapping) BMP installation in the treatment subwatersheds. In Spring Creek, BMPs significantly improved overall stream habitat quality, bank stability, instream cover for fish, abundance of cool‐ and coldwater fishes, and abundance of all fishes. Improvements were most pronounced at sites with riparian BMPs. Water temperatures were consistently cold enough to support coldwater fishes such as trout (Salmonidae) and sculpins (Cottidae) even before BMP installation. We observed the first‐time occurrence of naturally reproduced brown trout (Salmo trutta) in Spring Creek, indicating that the stream condition had been improved to be able to partially sustain a trout population. In Eagle Creek and its tributary Joos Creek, limited riparian BMPs led to localized gains in overall habitat quality, bank stability, and water depth. However, because few upland BMPs were installed in the subwatershed there were no improvements in water temperature or the quality of the fish community. Temperatures remained marginal for coldwater fish throughout the study. Our results demonstrate that riparian BMPs can improve habitat conditions in Wisconsin streams, but cannot restore coldwater fish communities if there is insufficient upland BMP implementation. Our approach of studying multiple paired treatment and reference streams before and after BMP implementation proved effective in detecting the response of stream ecosystems to watershed management activities.     

Delayed Flood Recession in Central Yangtze Floodplains Can Cause Significant Food Shortages for Wintering Geese: Results of Inundation Experiment

Carex meadows are critical habitat for wintering geese in the floodplains of the middle and lower reaches of Yangtze River, China. These meadows follow a growth cycle closely tied to the seasonal hydrological fluctuation: as water levels recede in the fall, exposed mudflats provide habitat for Carex spp. growth. The seasonal growth of Carex overlaps the arrival of wintering geese and provides an important food source for the migrants. Recent alterations to the Yangtze’s hydrology, however, have disrupted the synchronous relationship between water levels, Carex growth and wintering geese at Dongting Lake. In October 2012, we carried out an outdoor mesocosm experiment to investigate potential impacts of delayed water recession on the germination and growth of Carex heterolepis, the dominant Carex species at Dongting Lake, to understand how changes in hydrology might impact wintering goose habitat. Results showed that the delayed flood recession exerted significant impact on the first growth cycle of Carex growth. Prolonged inundation significantly lowered the intrinsic growth rate (P = 0.03) and maximum growth rates (P = 0.02). It also took significantly longer time to reach the peak growth rate (P = 0.04 and 0.05 for number of shoot and biomass, respectively). As a result, biomass accumulation was reduced by 45, 62 and 90 % for 10-day, 20-day and 30-day inundation treatments, respectively. These results indicate a severe risk of food shortage for wintering geese when water recession delayed. This potential risk should be taken into consideration when operating any hydrological control structures that alter the flood regimes in Dongting Lake.     

Spatial and Temporal Patterns in Fish Assemblages Following an Artificially Extended Floodplain Inundation Event, Northern Murray-Darling Basin, Australia

Water extraction from dryland rivers is often associated with declines in the health of river and floodplain ecosystems due to reduced flooding frequency and extent of floodplain inundation. Following moderate flooding in early 2008 in the Narran River, Murray-Darling Basin, Australia, 10,423 ML of water was purchased from agricultural water users and delivered to the river to prolong inundation of its terminal lake system to improve the recruitment success of colonial waterbirds that had started breeding in response to the initial flooding. This study examined the spatial and temporal patterns of fish assemblages in river and floodplain habitats over eight months following flooding to assess the possible ecological benefits of flood extension. Although the abundances of most fish species were greater in river channel habitats, the fish assemblage used floodplain habitats when inundated. Young-of-the-year (4–12 months age) golden perch (Macquaria ambigua) and bony bream (Nematalosa erebi) were consistently sampled in floodplain sites when inundated, suggesting that the floodplain provides rearing habitat for these species. Significant differences in the abundances of fish populations between reaches upstream and downstream of a weir in the main river channel indicates that the effectiveness of the environmental water release was limited by restricted connectivity within the broader catchment. Although the seasonal timing of flood extension may have coincided with sub-optimal primary production, the use of the environmental water purchase is likely to have promoted recruitment of fish populations by providing greater access to floodplain nursery habitats, thereby improving the ability to persist during years of little or no flow.     

A Spatially Explicit Resource-Based Approach for Managing Stream Fishes in Riverscapes

The article describes a riverscape approach based on landscape ecology concepts, which aims at studying the multiscale relationships between the spatial pattern of stream fish habitat patches and processes depending on fish movements. A review of the literature shows that few operational methods are available to study this relationship due to multiple methodological and practical challenges inherent to underwater environments. We illustrated the approach with literature data on a cyprinid species (Barbus barbus) and an actual riverscape of the Seine River, France. We represented the underwater environment of fishes for different discharges using two-dimensional geographic information system-based maps of the resource habitat patches, defined according to activities (feeding, resting, and spawning). To quantify spatial patterns at nested levels (resource habitat patch, daily activities area, subpopulation area), we calculated their composition, configuration, complementation, and connectivity with multiple spatial analysis methods: patch metrics, moving-window analysis, and least cost modeling. The proximity index allowed us to evaluate habitat patches of relatively great value, depending on their spatial context, which contributes to the setting of preservation policies. The methods presented to delimit potential daily activities areas and subpopulation areas showed the potential gaps in the biological connectivity of the reach. These methods provided some space for action in restoration schemes.