Studies that evaluate the linkages between watershed improvement through Best Management Practices (BMPs) and downstream outcomes are few. Water quality of coastal waters is often impacted by soil and nutrient loss from watersheds in agriculture. Mitigation of these impacts is of concern in the Great Lakes, the Finger Lakes Region of New York State, and generally in water bodies of North America. In this issue, we report on hypothesis-based research at the watershed level evaluating the impact of BMPs on mitigation of nonpoint sources of nutrient and soil loss to streams and the nearshore zone of a lake. Specifically, we hypothesize not only reductions in nutrient and soil losses from watersheds but also a resultant decrease in metaphyton (filamentous algae), coliform bacteria, and macrophyte populations in the nearshore at stream mouths draining sub-watersheds where BMPs were introduced. Small experimental sub-watersheds, predominantly in agriculture (>70%), were selected to ensure that effects on downstream systems would not be confounded by other land use practices often observed in large watershed approaches. In this introductory paper, we provide background information on Conesus Lake, its watershed, and the Conesus Lake watershed project, a large multi-disciplinary study evaluating agricultural management practices. The series of papers in this volume consider the effect of BMPs designed to control nonpoint sources on water chemistry, metaphyton, macrophytes, and microbial populations in the coastal zone of a lake. Ultimately, this volume expands the basic understanding of the ability of BMPs to control nonpoint source pollution while contributing toward the goal of improving water quality of downstream systems including streams, embayments, and the nearshore of large lakes.

Conesus Lake and its agricultural watershed exemplify many of the challenges of effectively managing land and water resources for multiple uses. One of the smaller of New York's Finger Lakes, Conesus Lake is eutrophic with abundant growth of rooted aquatic plants and algae. The trophic condition of the lake has been relatively stable for decades as measured by phosphorus concentrations and hypolimnetic dissolved oxygen depletion rates. However, recent changes to the lake ecosystem have led to diminished water clarity, higher density of macrophytes in shallower water, and the proliferation of nearshore macroalgae. These water quality changes caused serious concern regarding the ultimate causes of the degradation; community conflict was evident between the upland agricultural producers and shoreline residents. With funding from the New York State Department of State, Livingston County Planning Department led a successful effort to engage the community in a science-based assessment of the interrelationship of land use and lake water quality. The planning process was designed to develop consensus that the lake is a shared resource and that effective solutions require changes by many stakeholders. The outcome of this effort was the Conesus Lake Watershed Management Plan. An intermunicipal Conesus Lake Watershed Council was formed to implement the plan's recommendations. The Council has been active for 5 years and has weathered two local elections with full community support. Although many factors contribute to the success of this watershed planning initiative, the importance of a science-based foundation and ongoing efforts to build political consensus cannot be overstated.

Small sub-watersheds of the Conesus Lake catchment were the site of a project evaluating the ability of agricultural Best Management Practices (BMPs) to maintain soil and nutrients on the landscape and to reduce the impact of agriculture on downstream aquatic systems. Local agricultural agencies, with participation of local farmers, joined with scientists to focus attention on watershed issues, to develop and foster a sense of stewardship among the farming community, and to assist and coordinate collaboration among academic researchers, governing bodies, and the agricultural community. Cornell Cooperative Extension served as a liaison and as a resource and assisted in the development and implementation of voluntary BMPs in selected sub-watersheds of Conesus Lake. We discuss our approach to working with producers, the selection of watersheds for management, and our decision-making process for implementation of BMPs. Decisions to establish traditional structural and nonstructural management practices on sub-watersheds of Conesus Lake were based on field assessments, soil testing, the Phosphorus Index, and the software package Cornell Cropware. For example, the use of soil testing and the Cornell Cropware software allowed the cooperating farms to apply fertilizer only as needed for optimum crop production. Farmers achieved cost savings because previous plans had not given enough credit to soil reserves, manure, and sod crop nutrients. Low-cost voluntary practices based on well-established agricultural management practices have been combined with cost-shared (structural) practices in Conesus Lake watersheds to mitigate the impact of agricultural runoff on water quality and to improve cost efficiency of agricultural operations.

Six small, predominantly agricultural (>70%) watersheds in the Conesus Lake catchment of New York State, USA, were selected to test the impact of Best Management Practices (BMPs) on mitigation of nonpoint nutrient sources and soil loss from farms to downstream aquatic systems. Over a 5-year period, intensive stream water monitoring and analysis of covariance provided estimates of marginal means of concentration and loading for each year weighted by covariate discharge. Significant reductions in total phosphorus, soluble reactive phosphorus, nitrate, total Kjeldahl nitrogen, and total suspended solids concentration and flux occurred by the second year and third year of implementation. At Graywood Gully, where Whole Farm Planning was practiced and a myriad of structural and cultural BMPs were introduced, we observed the greatest percent reduction (average = 55.8%) and the largest number of significant reductions in analytes (4 out of 5). Both structural and cultural BMPs were observed to have profound effects on nutrient and soil losses. Where fields were left fallow or planted in a vegetative type crop, reductions, especially in nitrate, were observed. Where structural implementation occurred, reductions in total fractions were particularly evident. Where both were applied, major reductions in nutrients and soil occurred. After 5 years of management, nonevent and event concentrations of total suspended solids in streams draining agricultural watersheds were not significantly different from those in a relatively “pristine/reference” watershed. This was not the case for nutrients.

Nonpoint source pollution (NPSP) is the export to receiving waters of nutrients originating from diffuse sources. This research documents a methodology for confirming reductions in NPSP resulting from implementation of agricultural Best Management Practices (BMPs). It employs that methodology to confirm the success of BMPs implemented in Graywood Gully, a study sub-watershed that drains into Conesus Lake, NY. Evaluating the effects of BMPs in agricultural watersheds is often complicated by significant temporal variability in weather and hydrologic conditions. In many cases NPSP demonstrates much greater variability in response to antecedent hydrologic/ meteorologic conditions than to commonly implemented BMPs. In essence, weather variability can mask the beneficial effects of the BMPs. By using the Thornthwaite-Mather procedure to model soil moisture status in addition to event rainfall total, it is possible to remove the major sources of weather/hydrologic-related variability, essentially reducing the number of experimental variables to the BMP itself. Application of this method to the Graywood sub-watershed reveals that BMPs can greatly reduce export of NPSP generated pollutants to receiving waters. Estimates of NPSP reductions range from 53% for soluble reactive phosphorus to 89% for nitrate.

Whole Farm Planning was instituted and monitored over a 5-year period within the Graywood Gully sub-watershed of Conesus Lake, NY (USA). An array of agricultural Best Management Practices (BMPs) (strip cropping, fertilizer reduction, tiling, manure disposal practices, etc.) were simultaneously introduced to determine the impact of a concentrated management effort on nutrient and soil loss from one watershed within the Conesus Lake catchment. During the study period, significant decreases in winter concentrations of dissolved and particulate fractions, including total phosphorus (TP), soluble reactive phosphorus (SRP), total Kjeldahl nitrogen (TKN), and nitrate (NO₃) but not total suspended solids (TSS), were observed. These decreases may or may not be attributed to cessation of manuring practices. Three years into the study, an opportunity existed to test the responsiveness of the watershed to the curtailment of a single BMP — winter manure application to fields. We field-tested the hypothesis that a change in winter manure applications would impact dissolved and particulate fractions in stream water draining this watershed. We found that the water quality of Graywood Gully is very responsive to winter manure application on environmentally sensitive portions of the sub-watershed. With the short-term resumption of manure application, TP, SRP, TKN, and NO₃ concentrations rose dramatically in stream water; elevated phosphorus concentrations persisted over a 5-week period. Total suspended solids, however, were not elevated after short-term manure application. Factors that affected these results were slope of the land, application of manure over snow and during a snowfall, warm air and soil temperatures, and possibly tile drainage of snowmelt water. Managers of agricultural systems must recognize that phosphorus losses from the watershed during the nongrowing season may detrimentally affect nuisance population of algae in lakes during the summer.

Phosphorus sources within the Graywood Gully watershed impact water quality within the stream and receiving waters of Conesus Lake, New York. A mass balance approach was instructive in demonstrating the semi-quantitative impact of nonpoint and point nutrient sources on downstream aquatic systems and provided a mechanism to assist in targeting and prioritizing structural best management practices (BMPs) for agricultural areas. The identification and quantification of these sources reveal substantial sources coming from outside the topographic watershed boundary due to the overprint of the built environment on natural surface runoff pathways. The analysis of water sources and phosphorus loading indicated the importance of critical source areas in the watershed and adjacent areas and the effect of the built environment, including drain systems and road ditches, on changing critical hydrological pathways. The impact of BMPs within the watershed was masked by the external contributions from the “extended” watershed, adding over 40% of the total P load to Conesus Lake. This result suggests that the lack of significant decrease in dissolved phosphorus observed in the heavily managed Graywood sub-watershed is a result of not considering the “extended” watershed.

The movement of phosphorus (P) from agricultural fields to streams and deposition in the nearshore of the lake presents a continuum of related physical and chemical properties that act to partition P into different physico-chemical fractions. We investigated changes in soil and sediment P fractionation as material was eroded from predominantly agricultural fields, transported via stream sediments, and deposited in a nearshore lake environment. Total phosphorus content of the soils and sediment decreased from field soils with an average concentration of 553.81 mg P kg^-1 to 202.28 mg P kg^-1 in stream sediments to 67.47 mg P kg^-1 in lake sediments. Significant changes in P fractionation occurred during erosion, transport, and deposition of the particulate or sediment phase. The fractionation of P within the soils and sediments changed significantly from aluminum and organic matter associated P dominant in field soils to calcium associated P dominant in nearshore lake sediments. Various physical and chemical processes appear to be responsible for these transformations which impact the mobility and bioavailability of P. A significant amount of P was lost from field soils as they were transported and deposited. This P has either become available to biota or deposited in deeper portions of the lake system. Ultimately, the impact of P export on the nearshore lake environment may be influenced by the changes in P fractionation that occurred during transport and deposition and by the influence of macrophytes on the biogeochemical cycling of P in the sediment.

The microbiology of stream water has a seasonal component that results from both biogeochemical and anthropogenic processes. Analysis of nonevent conditions in streams entering Conesus Lake, NY (USA), indicated that total coliform, Escherichia coli, and Enterococcus spp. levels peak in the summer in all streams, independent of the agricultural use in the stream sub-watershed. Prior to implementation of management practices, E. coli in water draining Graywood Gully, a sub-watershed with 74% of the land in agriculture, reached as high as 2806 CFU/100 mL, exceeding the 235 CFU/100 mL EPA Designated Bathing Beach Standard (EPA-DBBS). In contrast, North McMillan Creek, a sub-watershed with <13% of its land in agriculture, had E. coli maxima generally near or below the EPA-DBBS. Graywood Gully at times had a higher microbial loading than North McMillan Creek, a sub-watershed 48 times larger in surface area. Over a 5-year study period, there was a major decrease in bacterial loading during nonevent conditions at Graywood Gully, especially after manure management practices were implemented, while bacterial loading was constant or increased in streams draining three other sub-watersheds. E. coli levels dropped more than 10 fold to levels well below the EPA-DBBS while the yearly maximum for Enterococcus dropped by a factor 2.5. Similarly, exceedency curves for both E. coli and Enterococcus also showed improvement since there were fewer days during which minimum standards were exceeded. Even so, Graywood Gully at times continued to be a major contributor of E. coli to Conesus Lake. If wildlife represents a significant source of indicator bacteria to Graywood Gully as has been reported, stream remediation, management efforts and compliance criteria will need to be adjusted accordingly.

Both storm water event and nonevent flow contributed to the annual discharge from Graywood Gully, a small sub-watershed of Conesus Lake, New York USA, whose land use is 74% agriculture. While events contributed significant amounts of water in short periods of time, nonevents accounted for the majority of water on a yearly basis and could have flow rates matching those that occurred during events. Event storm water was elevated in materials associated with particulates such as total suspended solids, total Kjeldahl nitrogen, and total phosphorus. Water from high flow nonevents was elevated in soluble components such as sodium, nitrate, and soluble reactive phosphorus. As a result, events contributed the majority of particulates to the yearly loading from Graywood Gully whereas nonevents contributed the majority of soluble materials. The levels of total coliforms, Escherichia coli, Enterococcus, and total heterotrophic bacteria were elevated in storm water relative to nonevent flow, indicating that they acted as particulates. The median level of E. coli in nonevents was 200 CFU/100 mL whereas the median level during events was 3660 CFU/100 mL. Consequently, storm events accounted for 92% of all E. coli loading from Graywood Gully. Best Management Practices (BMPs) resulted in the mean, median, maximum and minimum levels of event-driven E. coli loading from Graywood Gully to decrease 10 fold over a 5-year period. The implementation of BMPs in the Graywood Gully watershed has improved the microbiology of event waters and consequently decreased the role that the watershed plays as a contributor of microbial pollution to Conesus Lake.

Cyanotoxins, a group of hepatotoxins and neurotoxins produced by cyanobacteria, pose a health risk to those who use surface waters as sources for drinking water and for recreation. Little is known about the spatial and seasonal occurrence of cyanotoxins in Lake Ontario and other lakes and ponds within its watershed. Within the embayments, ponds, rivers, creeks, shoreside, and nearshore and offshore sites of Lake Ontario, microcystin-LR concentrations were low in May, increased through the summer, and reached a peak in September before decreasing in October. Considerable variability in microcystin-LR concentrations existed between and within habitat types within the Lake Ontario ecosystem. In general, the average microcystin-LR concentration was two orders of magnitude lower in embayment (mean = 0.084 µg/L), river (mean = 0.020 µg/L), and shoreside (mean = 0.052 µg/L) sites compared to upland lakes and ponds (mean = 1.136 µg/L). Concentrations in the nearshore sites (30-m depth) and offshore sites (100-m depth) were another order of magnitude lower (mean = 0.006 µg/L) than in the creek/river, bay/pond, and shoreside habitats. Only 0.3% (2 of 581) of the samples taken in Lake Ontario coastal waters exceeded the World Health Organization (WHO) Drinking Water Guideline of 1 µg microcystin/L for humans. In contrast, 20.4% (20 of 98) of the samples taken at upland lakes and ponds within the watershed of Lake Ontario exceeded WHO Guidelines. No significant relationship between nitrate and microcystin-LR concentrations was observed in Lake Ontario even though a significant positive relationship existed between phosphorus and phycocyanin and microcystin-LR concentrations. At an upland lake site (Conesus Lake) in the Ontario watershed, the development of a littoral Microcystis population was not observed despite high nutrient loading (P and N) into the nearshore zone, well-developed nearshore populations of filamentous Spirogyra and Zygnema, the occurrence of Dreissena spp., and the known occurrence of Microcystis and microcystin production in the pelagic waters of Conesus Lake.

Filamentous algal cover was quantified during periods of peak biomass from 2001 to 2007 in six littoral macrophyte beds in Conesus Lake, New York (USA). Three of the study sites were adjacent to streams that drained sub-watersheds where extensive agricultural best management practices (BMPs) designed to reduce nutrient runoff were implemented beginning in 2003. Three other study sites were downstream from sub-watersheds where only a few or no BMPs were implemented by landowners. For the sites that received extensive management, comparisons of the Pre-BMP baseline period (2–3 yrs) to the Post-BMP period (4 yrs) revealed that algal cover was statistically lower than baseline in eight of eleven years (72.7%). For the three sites where limited or no management was implemented, the percent cover of filamentous algae was lower than Pre-BMP baseline levels in only three of twelve years (25%). Where major reductions in cover of filamentous algae occurred, positive relationships existed with summer stream loading of nitrate and soluble reactive phosphorus to the nearshore. In some cases only nitrate loading was significantly correlated with percent cover, indicating that the relative importance of nitrogen and phosphorus to algal growth near streams may be determined by the characteristics and land use within each sub-watershed. Agricultural BMPs targeting nutrient and suspended solid runoff can effectively reduce filamentous algal growth locally along the lake littoral zone on a time scale of months to a few years and with moderate commitment of resources. This work offers a new perspective for management of the growing problem of littoral algal growth in the embayments and drowned river mouths of the Great Lakes.

Long-term studies of macrophyte beds growing near streams in Conesus Lake, New York, have revealed a high biomass and continuing dominance of the invasive rooted species Eurasian watermilfoil (Myriophyllum spicatum). We tested whether agricultural best management practices (BMPs) designed to reduce tributary nutrient and soil loss from the watershed could reduce populations of Eurasian watermilfoil downstream in the lake littoral. Six macrophyte beds were monitored during a 3-year baseline period (2001–2003) prior to the implementation of BMPs and for a 4-year experimental period after a variety of agricultural BMPs were implemented in three sub-watersheds. For three macrophyte beds downstream from sub-watersheds managed as part of our project, quadrat biomass decreased by 30–50% and was statistically lower than Pre-BMP baseline values in 7 of 11 experimental sample years. Biomass loss primarily in the form of the dominant Eurasian watermilfoil ranged from 6.2 to 10 t wet weight for each bed. The declines in biomass coincided with significant annual and January—August decreases in the concentrations and fluxes of dissolved nutrients, total phosphorus, and total suspended solids in nearby streams. For three macrophyte beds downstream from watersheds in which landowners applied less extensive or no new agricultural management, biomass was statistically indistinguishable from Pre-BMP baseline values in all 12 experimental sample years. Milfoil remained the overwhelmingly dominant species at all sites during the entire study period. These results provide impetus for the use of watershed nutrient management to control the nuisance growth of Eurasian Watermilfoil on a local scale in the lake littoral.

Recent studies in Conesus Lake, New York, documented significant decreases in the biomass of Eurasian watermilfoil (Myriophyllum spicatum) near the mouths of streams draining sub-watersheds where reductions in nutrient loading occurred as a result of the implementation of agricultural Best Management Practices (BMPs). In situ experiments were conducted to further investigate the relationship between stream loading, foliar uptake, and growth of Eurasian watermilfoil. In two of three experiments, plants cropped to a height of approximately 50 cm had the lowest growth (g/m²) downstream from a sub-watershed where major BMPs had been implemented (80% and 0%). In sub-watersheds where minimal or no BMPs were introduced, plants showed significantly higher growth as biomass increased (216% and 22%). In a second set of experiments, shoots of Eurasian watermilfoil plants were incubated for 24 h in ambient lake water and in lake water with enriched concentrations of nitrate and soluble reactive phosphorus comparable to rain event stream effluent concentrations and then allowed to grow in situ for a 2-week experimental period. For all experiments combined, the shoot biomass increased significantly in the enhanced nutrient treatments when compared to the ambient treatment at the Sand Point macrophyte bed (reduced loading) but not at the Eagle Point macrophyte bed (high loading). Overall, the results indicate that foliar uptake of nutrients in stream effluent can contribute to the growth of Eurasian watermilfoil and reinforce the hypothesis that reductions in stream loading through agricultural BMPs can help reduce macrophyte growth in the lake littoral.