Delta Marsh is a 19,000-hectare freshwater coastal wetland located on the southern shore of Lake Manitoba, Canada. The ecological integrity of Delta Marsh has been declining due to changes in hydrology, nutrient loading, water quality and the introduction of invasive species. Research on variables influencing this decline is imperative for restoration. The objectives of this research were to determine which chemical and physical variable(s) drive phytoplankton chlorophyll-a concentrations and to determine if there is spatial variation of nutrient loading caused by the land use gradient across the watershed. Environmental variables were analyzed using multivariate statistical analyses and demonstrated that phytoplankton blooms were most influenced by meteorological conditions and nutrient availability. Nutrient exports to Delta Marsh were greater in areas with higher agricultural cover. This research will help inform management plans to restore the ecological function to Delta Marsh and other coastal wetlands, ultimately improving water quality, fisheries and waterfowl habitat.