Chesapeake Bay eutrophication: scientific understanding, ecosystem restoration, and challenges for agriculture

Chesapeake Bay has been the subject of intensive research on cultural eutrophication and extensive efforts to reduce nutrient inputs. In 1987 a commitment was made to reduce controllable sources of nitrogen (N) and phosphorous (P) by 40% by the year 2000, although the causes and effects of eutrophication were incompletely known. Subsequent research, modeling, and monitoring have shown that: (i) the estuarine ecosystem had been substantially altered by increased loadings of N and P of approximately 7- and 18-fold, respectively; (ii) hypoxia substantially increased since the 1950s; (iii) eutrophication was the major cause of reductions in submerged vegetation; and (iv) reducing nutrient sources by 40% would improve water quality, but less than originally thought. Strong public support and political commitment have allowed the Chesapeake Bay Program to reduce nutrient inputs, particularly from point sources, by 58% for P and 28% for N. However, reductions of nonpoint sources of P and N were projected by models to reach only 19% and 15%, respectively, of controllable loadings. The lack of reductions in nutrient concentrations in some streams and tidal waters and field research suggest that soil conservation-based management strategies are less effective than assumed. In 1997, isolated outbreaks of the toxic dinoflagellate Pfiesteria piscicida brought attention to the land application of poultry manure as a contributing factor to elevated soil P and ground water N concentrations. In addition to developing more effective agricultural practices, emerging issues include linking eutrophication and living resources, reducing atmospheric sources of N, enhancing nutrient sinks, controlling sprawling suburban development, and predicting and preventing harmful algal blooms.     

Interactions of warming and altered nutrient load timing on the phenology of oxygen dynamics in Chesapeake Bay

The effects of nutrient loading on estuaries are well studied, given the multitude of negative water quality and ecosystem effects that have been attributed to excess nitrogen and phosphorus. A current gap in this knowledge involves the sensitivity of seasonal cycles of estuarine biogeochemical processes to direct (warming) and indirect influences (nutrient load timing) of climate change. We used a coupled hydrologic–biogeochemical model to investigate changes in the phenology of hypoxia and related biogeochemical processes in Chesapeake Bay under three different hydrologic regimes. Shifts to earlier nutrient load timing during idealized simulations reduced the overall annual hypoxic volume, resulting from discernable, but relatively small reductions in phytoplankton biomass and both sediment and water-column respiration. Simulated increases in water temperature caused an increase in spring/early summer hypoxic volume associated with elevated respiration rates, but an associated exhaustion of organic matter in the early summer caused a decrease in late summer/fall hypoxic volume due to lowered respiration. Warming effects on hypoxia were larger than nutrient timing effects in scenarios where warming was restricted to spring and when it was applied to all months of the year. These idealized simulations begin the process of understanding the potential impacts of future climatic changes in the seasonal timing of key biogeochemical processes associated with eutrophication.     

Estimating Relevance of Organic Carbon,Nitrogen, and Phosphorus Loads to a Blackwater River Estuary1

Abstract: In blackwater river estuaries, a large portion of external carbon, nitrogen, and phosphorus load are combined in complex organic molecules of varying recalcitrance. Determining their lability is essential to establishing the relationship between anthropogenic loads and eutrophication. A method is proposed in which organic C, N, and P are partitioned into labile and refractory forms, based upon first‐order decay estimated by biochemical oxygen demand relative to total organic carbon, and C:N and C:P ratios as a function of organic carbon lability. The technique was applied in developing total maximum daily loads for the lower St. Johns, a blackwater Atlantic coastal plain river estuary in Northeast Florida. Point source organic nutrients were determined to be largely labile. Urban runoff was found to have the highest relative labile organic N and P content, followed by agricultural runoff. Natural forest and silviculture runoff were high in refractory organic N and P. Upstream labile C, N, and P loads were controlled by autochthonous production, with 34‐50% of summer total labile carbon imported as algal biomass. Differentiation of labile and refractory organic forms suggests that while anthropogenic nutrient enrichment has tripled the total nitrogen load, it has resulted in a 6.7‐fold increase in total labile nitrogen load.     

NUTRIENT LOADS TO WISCONSIN LAKES: PART II. RELATIVE IMPORTANCE OF NUTRIENT SOURCES1

ABSTRACT: A comparison of municipal wastewater treatment plant (WWTP) and nonpoint source nutrient loads to Wisconsin's 14,927 inland lakes was performed. Only 65 of the 2,925 Wisconsin lakes having surface areas of at least eight ha and a maximum depth of at least 2.4 m had one or more WWTP's located within 40 km upstream; 99 of Wisconsin's 477 WWTP's were identified to be upstream of these 65 lakes. WWTP total nitrogen and total phosphorus loads to these 65 lakes were estimated using per capita influent loads and removal efficiencies based on wastewater treatment types. Nonpoint source nutrient loads were calculated utilizing nutrient export coefficients derived specifically for Wisconsin. Total nitrogen inputs to the lakes were dominated by nonpoint sources. The effectiveness of various phosphorus control programs to produce water quality improvements visible to the public was estimated to be as follows (going from most to least effective): municipal phosphorus removal and agricultural reductions, municipal phosphorus removal alone, agricultural reduction plus phosphate detergent ban, agricultural reductions alone, and phosphate detergent ban alone. The last option would not be expected to produce water quality improvement visible to the public in any Wisconsin lakes. The differences between the distributions in Wisconsin of population and inland lakes highlights the need to consider regional characteristics in any statewide water quality management plan.     

Temporal and Spatial Trends in Nutrient and Sediment Loading to Lake Tahoe,California‐Nevada,USA

Since 1980, the Lake Tahoe Interagency Monitoring Program (LTIMP) has provided stream‐discharge and water quality data—nitrogen (N), phosphorus (P), and suspended sediment—at more than 20 stations in Lake Tahoe Basin streams. To characterize the temporal and spatial patterns in nutrient and sediment loading to the lake, and improve the usefulness of the program and the existing database, we have (1) identified and corrected for sources of bias in the water quality database; (2) generated synthetic datasets for sediments and nutrients, and resampled to compare the accuracy and precision of different load calculation models; (3) using the best models, recalculated total annual loads over the period of record; (4) regressed total loads against total annual and annual maximum daily discharge, and tested for time trends in the residuals; (5) compared loads for different forms of N and P; and (6) tested constituent loads against land use‐land cover (LULC) variables using multiple regression. The results show (1) N and P loads are dominated by organic N and particulate P; (2) there are significant long‐term downward trends in some constituent loads of some streams; and (3) anthropogenic impervious surface is the most important LULC variable influencing water quality in basin streams. Many of our recommendations for changes in water quality monitoring and load calculation methods have been adopted by the LTIMP.     

Recent Cattail Expansion and Possible Relationships to Water Management: Changes in Upper Taylor Slough (Everglades National Park,Florida, USA)

Recent appearance of cattail (Typha domingensis) within a southern Everglades slough—Upper Taylor Slough (Everglades National Park)—suggests ecosystem eutrophication. We analyze water quality, nutrient enrichment, and water management operations as potential drivers of eutrophication in Upper Taylor Slough. Further, we attempt to determine why surface water phosphorus, a parameter used commonly to monitor ecosystem health in the Everglades, did not serve as an early warning for eutrophication, which has broader implication for other restoration efforts. We found that surface water total phosphorus concentrations generally were below a 0.01 mg L⁻¹ threshold determined to cause imbalances in flora and fauna, suggesting no ecosystem eutrophication. However, assessment of nutrient loads and loading rates suggest Upper Taylor Slough has experienced eutrophication and that continued total phosphorus loading through a point-source discharge was a major driver. These nutrient loads, combined with increases in hydroperiods, led to the expansion of cattail in Upper Taylor Slough. We recommend other metrics, such as nutrient loads, periphyton and arthropod community shifts, and sediment core analyses, for assessing ecosystem health. Monitoring surface water alone is not enough to indicate ecosystem stress.     

The Macquarie Marshes in Arid Australia and their waterbirds: A 50-year history of decline

We investigated the relationship between total annual flow of water in the Macquarie River and the extent of flooding in the northern part of the Macquarie Marshes and trends in waterbird populations from 1983 to 1993. The amount of water in the Macquarie River measured each year within the Macquarie Marshes explained about 86% of the variation in area flooded in the northern part of this wetland. This allowed use of long-term data on flow at Oxley, a gauge within the Macquarie Marshes, as an index to flooding. Annual flows at Oxley have decreased significantly for high and medium rainfall events in the catchment, despite no trend in rainfall between 1944 and 1993. The area flooded by large floods has contracted by at least 40–50% during the last 50 years (1944–1993). Water use has progressively increased upstream in the period, depriving the Macquarie Marshes of water: 51% of all water passing Dubbo each year, a gauge 100 km upstream, reached the Macquarie Marshes in the period 1944–1953, but by 1984–1993 this had declined to 21%. Numbers of species and density of waterbirds on the northern part of the Macquarie Marshes declined between 1983 and 1993. Three other wetlands, not affected by water abstractions, showed no declines. We believe the decline was due to wetland degradation as a result of decreased flooding. We estimated more than 88,000 waterbirds in the Macquarie Marshes in October 1984, establishing the site as an important wetland site in Australia. The extent and viability of this wetland will depend on maintaining or increasing the water supply.     

Assessing watershed transport of atrazine and nitrate to evaluate conservation practice effects and advise future monitoring strategies

Continued public support for U.S. taxpayer funded programs aimed at reducing agricultural pollutants depends on clear demonstrations of water quality improvements. The objective of this research was to determine if implementation of agricultural best management practices (BMPs) in the Goodwater Creek Experimental Watershed (GCEW) resulted in changes to atrazine and nitrate (NO₃–N) loads during storm events. An additional objective was to estimate future monitoring periods necessary to detect a 5, 10, 20, and 25% reduction in atrazine and NO₃–N event load. The GCEW is a 73 km² watershed located in northcentral Missouri, USA. Linear regressions and Akaike Information Criteria were used to determine if reductions in atrazine and NO₃–N event loads occurred as BMPs were implemented. No effects due to any BMP type were indicated for the period of record. Further investigation of event sampling from the long-term GCEW monitoring program indicated errors in atrazine load calculations may be possible due to pre-existing minimum threshold levels used to trigger autosampling and sample compositing. Variation of event loads was better explained by linear regressions for NO₃–N than for atrazine. Decommissioning of upstream monitoring stations during the study period represented a missed opportunity to further explain variation of event loads at the watershed outlet. Atrazine requires approximately twice the monitoring period relative to NO₃–N to detect future reductions in event load. Appropriate matching of pollutant transport mechanisms with autosampling protocols remains a critical information need when setting up or adapting watershed monitoring networks aimed at detecting watershed-scale BMP effects.     

Evaluation of Progress in Achieving TMDL Mandated Nitrogen Reductions in the Neuse River Basin, North Carolina

Management efforts to control excess algal growth in the Neuse River and Estuary, North Carolina began in the 1980s, with an initial focus on phosphorus (P) input reduction. However, continued water quality problems in the 1990s led to development of a Total Maximum Daily Load (TMDL) for nitrogen (N) in 1999 to improve conditions in N-sensitive estuarine waters. Evaluation of the effectiveness of management actions implemented in the Neuse River basin is a challenging endeavor due to natural variations in N export associated with climate. A simplified approach is presented that allows evaluation of trends in flow-normalized nutrient loading to provide feedback on effectiveness of implemented actions to reduce N loading to estuarine waters. The approach is applied to five watershed locations, including the headwaters of the Neuse Estuary. Decreases in nitrate + nitrite (NO₃–N) concentrations occurred throughout the basin and were largest just downstream of the Raleigh metropolitan area. Conversely, concentrations of total Kjeldahl N (TKN) increased at many stations, particularly under high flow conditions. This indicates a relative increase in organic N (Org-N) inputs since the mid-1990s. Overall, patterns in different N fractions at watershed stations indicate both partial success in reducing N inputs and ongoing challenges for N loading under high flow conditions. In downstream waters, NO₃–N concentrations decreased concurrent with TMDL implementation in the upper portion of the estuary but not in the middle and lower reaches. The lack of progress in the middle and lower reaches of the estuary may, at least in part, be affected by remineralization of settled particle-bound N deposited under high river flows.     

Long-Term Effects of Changing Land Use Practices on Surface Water Quality in a Coastal River and Lagoonal Estuary

The watershed of the Neuse River, a major tributary of the largest lagoonal estuary on the U.S. mainland, has sustained rapid growth of human and swine populations. This study integrated a decade of available land cover and water quality data to examine relationships between land use changes and surface water quality. Geographic Information Systems (GIS) analysis was used to characterize 26 subbasins throughout the watershed for changes in land use during 1992–2001, considering urban, agricultural (cropland, animal as pasture, and densities of confined animal feed operations [CAFOs]), forested, grassland, and wetland categories and numbers of wastewater treatment plants (WWTPs). GIS was also used together with longitudinal regression analysis to identify specific land use characteristics that influenced surface water quality. Total phosphorus concentrations were significantly higher during summer in subbasins with high densities of WWTPs and CAFOs. Nitrate was significantly higher during winter in subbasins with high numbers of WWTPs, and organic nitrogen was higher in subbasins with higher agricultural coverage, especially with high coverage of pastures fertilized with animal manure. Ammonium concentrations were elevated after high precipitation. Overall, wastewater discharges in the upper, increasingly urbanized Neuse basin and intensive swine agriculture in the lower basin have been the highest contributors of nitrogen and phosphorus to receiving surface waters. Although nonpoint sources have been emphasized in the eutrophication of rivers and estuaries such as the Neuse, point sources continue to be major nutrient contributors in watersheds sustaining increasing human population growth. The described correlation and regression analyses represent a rapid, reliable method to relate land use patterns to water quality, and they can be adapted to watersheds in any region.     

Estimating the Unknown Components of Nutrient Mass Balances for Forestry Plantations in Mine Rehabilitation, Upper Hunter Valley, New South Wales, Australia

Commercial forestry plantations as a postmining land use in the Upper Hunter Valley of New South Wales, Australia are restricted by both the poor nutrient availability of mining substrates and low regional rainfall. An experiment was conducted to investigate whether municipal waste products and saline groundwater from coal mining operations could improve early tree growth without impacting on the environment through salt accumulation and/or nutrient enrichment and changes in groundwater quality. Potential impacts were investigated by quantifying the nutrient cycling dynamics within the plantation using an input–output mass balance approach for exchangeable calcium (Ca²⁺), exchangeable magnesium (Mg²⁺), exchangeable potassium (K⁺), exchangeable sodium (Na⁺), nitrogen (N), and phosphorus (P). Measured inputs to and outputs from the available nutrient pool in the 0–30 cm of the overburden subsystem were used to estimate the net effect of unmeasured inputs and outputs (termed “residuals”). Residual values in the mass balance of the irrigated treatments demonstrated large leaching losses of exchangeable Ca, Mg, K, and Na. Between 96% and 103% of Na applied in saline mine-water irrigation was leached below the 0–30-cm soil profile zone. The fate of these salts beyond 30 cm is unknown, but results suggest that irrigation with saline mine water had minimal impact on the substrate to 30 cm over the first 2 years since plantation establishment. Accumulations of N and P were detected for the substrate amendments, suggesting that organic amendments (particularly compost) retained the applied nutrients with very little associated losses, particularly through leaching.     

Water-quality effectiveness of a detention/wetland treatment system and its effect on an urban lake

A newly installed combined detention/wetland stormwater treatment facility upstream from Lake McCarrons, Roseville, Minnesota, was monitored for 21 months to evaluate its effectiveness and the response of the lake to decreased phosphorus loads. The treatment facility consists of a 1.0-ha detention pond that discharges into a series of six constructed wetland “chambers.” Data from snowmelt and rainfall events are presented for several pollutants. Results show good reductions for most pollutants. Discussion on the facets of the system's operation are presented. Data from the lake show very little change in its water quality from three years prior to restoration (1984–1986) to three years following restoration (1987–1989): the lake's phosphorus and chlorophyll has actually increased.     

Nutrient Response Modeling in Falls of the Neuse Reservoir

In order to study system responses of Falls of the Neuse Reservoir (Falls Lake) to varied nutrient loadings, a coupled three-dimensional hydrodynamic and eutrophication model was applied. The model was calibrated using 2005 and 2006 intensive survey data, and validated using 2007 survey data. Compared with historical hydrological records, 2005 and 2007 were considered as dry years and 2006 was recognized as a normal year. Relatively higher nutrient fluxes from the sediment were specified for dry year model simulations. The differences were probably due to longer residence time and hence higher nutrient retention rate during dry years in Falls Lake. During the normal year of 2006, approximately 70% of total nitrogen (TN) and 80% of total phosphorus (TP) were delivered from the tributaries; about 20% (TN and TP) were from the sediment bottom. During the dry years of 2005 and 2007, the amount of TN released from sediment was equivalent to that introduced from the tributaries, indicating the critical role of nutrient recycling within the system in dry years. The model results also suggest that both nitrogen and phosphorus are limiting phytoplankton growth in Falls Lake. In the upper part of the lake where high turbidity was observed, nitrogen limitation appeared to dominate. Scenario model runs also suggest that great nutrient loading reductions are needed for Falls Lake to meet the water quality standard.     

Toward Reversal of Eutrophic Conditions in a Subtropical Estuary: Water Quality and Seagrass Response to Nitrogen Loading Reductions in Tampa Bay, Florida, USA

Coastal waters have been significantly influenced by increased inputs of nutrients that have accompanied population growth in adjacent drainage basins. In Tampa Bay, Florida, USA, the population has quadrupled since 1950. By the late 1970s, eutrophic conditions including phytoplankton and macroalgal blooms and seagrass losses were evident. The focus of improving Tampa Bay is centered on obtaining sufficient water quality necessary for restoring seagrass habitat, estimated to have been 16,400 ha in 1950 but reduced to 8800 ha by 1982. To address these problems, targets for nutrient load reductions along with seagrass restoration goals were developed and actions were implemented to reach adopted targets. Empirical regression models were developed to determine relationships between chlorophyll a concentrations and light attenuation adequate for sustainable seagrass growth. Additional empirical relationships between nitrogen loading and chlorophyll a concentrations were developed to determine how Tampa Bay responds to changes in loads. Data show that when nitrogen load reduction and chlorophyll a targets are met, seagrass cover increases. After nitrogen load reductions and maintenance of chlorophyll a at target levels, seagrass acreage has increased 25% since 1982, although more than 5000 ha of seagrass still require recovery. The cooperation of scientists, managers, and decision makers participating in the Tampa Bay Estuary Program’s Nitrogen Management Strategy allows the Tampa Bay estuary to continue to show progress towards reversing many of the problems that once plagued its waters. These results also highlight the importance of a multi-entity watershed management process in maintaining progress towards science-based natural resource goals.     

Nutrient and Phytoplankton Analysis of a Mediterranean Coastal Area

Identifying and quantifying the key anthropogenic nutrient input sources are essential to adopting management measures that can target input for maximum effect in controlling the phytoplankton biomass. In this study, three systems characterized by distinctive main nutrient sources were sampled along a Mediterranean coast transect. These sources were groundwater discharge in the Ahuir area, the Serpis river discharge in the Venecia area, and a submarine wastewater outfall 1,900 m from the coast. The study area includes factors considered important in determining a coastal area as a sensitive area: it has significant nutrient sources, tourism is a major source of income in the region, and it includes an area of high water residence time (Venecia area) which is affected by the harbor facilities and by wastewater discharges. We found that in the Ahuir and the submarine wastewater outfall areas, the effects of freshwater inputs were reduced because of a greater water exchange with the oligotrophic Mediterranean waters. On the other hand, in the Venecia area, the highest levels of nutrient concentration and phytoplankton biomass were attributed to the greatest water residence time. In this enclosed area, harmful dinoflagellates were detected (Alexandrium sp. and Dinophysis caudata). If the planned enlargement of the Gandia Harbor proceeds, it may increase the vulnerability of this system and provide the proper conditions of confinement for the dinoflagellate blooms’ development. Management measures should first target phosphorus inputs as this is the most potential-limiting nutrient in the Venecia area and comes from a point source that is easier to control. Finally, we recommend that harbor environmental management plans include regular monitoring of water quality in adjacent waters to identify adverse phytoplankton community changes.     

Lake eutrophication management modeling using dynamic programming

Lake eutrophication problems have received considerable attention in Taiwan, especially because they relate to the quality of drinking water. In this study, steady-state river water quality and lake eutrophication models are solved using dynamic programming algorithms to find the nutrient removal rates for eutrophication control during dry season. The kinetic cycle of chlorophyll-a, phosphorus and nitrogen for a complete-mixed lake is considered in the optimization framework. The Newton-iterative technique is adopted to solve the nonlinear equations for the steady-state lake eutrophication model. The optimization framework is applied to Cheng-Ching Lake in southern Taiwan. Several nutrient loading scenarios for eutrophication control are studied. Optimization results for nutrient removal rates and corresponding wastewater treatment capacities of each reach of the Kao-Ping River define the least cost approach to lake eutrophication control. A natural purification method, structural free water surface wetland, is also suggested to save more investment and improve river water quality at the same time.     

Multivariate analysis of paired watershed data to evaluate agricultural best management practice effects on stream water phosphorus

Quantification of the effects of management programs on water quality is critical to agencies responsible for water resource protection. This research documents reductions in stream water phosphorus (P) loads resulting from agricultural best management practices (BMPs) implemented as part of an effort to control eutrophication of Cannonsville Reservoir, a drinking water supply for New York City. Dairy farms in the upstate New York reservoir basin were the target of BMPs designed to reduce P losses. A paired watershed study was established on one of these farms in 1993 to evaluate changes in P loading attributable to implementation of BMPs that included manure management, rotational grazing, and improved infrastructure. Intensive stream water monitoring provided data to calculate P loads from the 160-ha farm watershed for all runoff events during a two-year pre-treatment period and a four-year post-treatment period. Statistical control for inter-annual climatic variability was provided by matched P loads from a nearby 86-ha forested watershed, and by several event flow variables measured at the farm. A sophisticated multivariate analysis of covariance (ANCOVA) provided estimates of both seasonal and overall load reductions. Statistical power and the minimum detectable treatment effect (MDTE) were also calculated. The results demonstrated overall event load reductions of 43% for total dissolved phosphorus (TDP) and 29% for particulate phosphorus (PP). Changes in farm management practices and physical infrastructure clearly produced decreases in event P losses measurable at the small watershed scale.     

The Contribution of Marsh Zones to Water Quality in Dutch Shallow Lakes: A Modeling Study

Many lakes have experienced a transition from a clear into a turbid state without macrophyte growth due to eutrophication. There are several measures by which nitrogen (N) and phosphorus (P) concentrations in the surface water can be reduced. We used the shallow lake model PCLake to evaluate the effects of three measures (reducing external nutrient loading, increasing relative marsh area, and increasing exchange rate between open water and marsh) on water quality improvement. Furthermore, the contribution of different retention processes was calculated. Settling and burial contributed more to nutrient retention than denitrification. The model runs for a typical shallow lake in The Netherlands showed that after increasing relative marsh area to 50%, total phosphorous (TP) concentration in the surface water was lower than the Maximum Admissible Risk (MAR, a Dutch government water quality standard) level, in contrast to total nitrogen (TN) concentration. The MAR levels could also be achieved by reducing N and P load. However, reduction of nutrient concentrations to MAR levels did not result in a clear lake state with submerged vegetation. Only a combination of a more drastic reduction of the present nutrient loading, in combination with a relatively large marsh cover (approximately 50%) would lead to such a clear state. We therefore concluded that littoral marsh areas can make a small but significant contribution to lake recovery.     

NONPOINT SOURCE DISCHARGES OF NUTRIENTS FROM PIEDMONT WATERSHEDS OF CHESAPEAKE BAY1

ABSTRACT: We measured annual discharges of water, sediments, and nutrients from 10 watersheds with differing proportions of agricultural lands in the Piedmont physiographic province of the Chesapeake Bay drainage. Flow-weighted mean concentrations of total N, nitrate, and dissolved silicate in watershed discharges were correlated with the proportion of cropland in the watershed. In contrast, concentrations of P species did not correlate with cropland. Organic P and C correlated with the concentration of suspended particles, which differed among watersheds. Thus, the ratio of N:P:Si in discharges differed greatly among watersheds, potentially affecting N, P or Si limitation of phytoplankton growth in the receiving waters. Simple regression models of N discharge versus the percentage of cropland suggest that croplands discharge 29–42 kg N ha^-1 yr^-1 and other lands discharge 1.2–5.8 kg N ha^-1 yr^-1. We estimated net anthropogenic input of N to croplands and other lands using county level data on agriculture and N deposition from the atmosphere. For most of the study watersheds, N discharge amounted to less than half of the net anthropogenic N.     

Analysis of Phytoplankton Community Structure Using Similarity Indices: A New Methodology for Discriminating Among Eutrophication Levels in Coastal Marine Ecosystems

Nine similarity indices based on phytoplankton community structure were examined for their sensitivity to assess different levels of eutrophication. Two phytoplankton data sets, one from an open coastal system and one from a semi-enclosed gulf, associated with different nutrient dynamics and circulation patterns were used for evaluating the indices. The results have shown that similarity indices, measuring interspecific association and resemblance of phytoplankton communities between enriched areas and control sites, were effective for detecting spatial and temporal dissimilarities in coastal marine ecosystems. The structure of the oligotrophic habitat as a potential source of ambiguity for the results was discussed, whereas the validity ranges and the potential applicability of this method were deemed to be dependent on the size of the fraction of the common species among the samples, and the similarity of the classification patterns resulted from this subcategory and those extracted from the overall community data. Furthermore, the study provides a new technique based on the use of the “Box and Whisker Plot” designed to distinguish opportunistic and rare phytoplanktonic species. The similarity indices, applied solely to the dominant species abundance, were more sensitive to resolve eutrophic, mesotrophic and oligotrophic conditions. This procedure can be proposed as an effective methodology for water characterization and can also be used as a qualitative tracer for detecting renewal processes of coastal marine ecosystems.