Over the past 40 years, hydroelectric, agricultural and urban watershed development and changing hydrology have transformed Lake Winnipeg into a highly eutrophic reservoir with annual outbreaks of widespread surface algal blooms, shoreline and net fouling, and concerns with intermittent cyanotoxin production. To provide a better understanding of the magnitude of these changes and the major causes, we examine long-term increases in phytoplankton biomass and shifts in phytoplankton species dominance in the context of both in-lake and watershed processes. We compare phytoplankton and water quality data from early (1969) and recent (1994–2007) lake-wide surveys, and information from paleolimnological analysis of sediment cores and satellite remote sensing. Our results demonstrate a recent and dramatic rise in severe algal blooms and increased dominance of cyanobacteria beginning in the mid-1990s, coincident with a large increase in phosphorous loading to the lake. Distinct increases in sediment core accumulation of nutrients and chlorophyll, cyanobacteria and diatom microfossils coincided with hydroelectric and agricultural development, increased Red R discharge and shifts in water transparency patterns across the lake. There has been a dramatic increase in phytoplankton biomass, accompanied by marked shifts in seasonal community composition. Spring diatoms blooms are of shorter duration and increasingly dominated by more eutrophic diatom taxa while summer blooms show reduced taxonomic diversity and an increased predominance of nitrogen-fixing cyanobacteria. Satellite images showed annual development of vast summer surface blooms, mainly in the north basin, with chlorophyll highest in regions of relatively low suspended sediment concentration and high transparency. There is an increasing dominance of potentially toxic cyanobacteria taxa and high levels of microcystins in nearshore samples of surface blooms. The combined effects of nutrient increases, algal species shifts and toxin production represent a potential threat to the sustainability of ecosystem function and productivity.

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