Farmington Bay of Great Salt Lake receives a significant amount of the nutrient-polluted runoff from Salt Lake and Davis Counties, Utah. This nutrient-laden runoff has led to seasonal blooms of blue-green algae, Nodularia spumigena, which produce a toxin called nodularin that has been shown to be toxic to aquatic organisms, birds, and mammals. Nodularia spumigena are the most common algae found in Farmington Bay. This study focused on understanding the physical and chemical factors controlling the growth of Nodularia spumigena in order to improve our knowledge about how nutrients impact algae in the Great Salt Lake. The salinity of the bay ranged from almost fresh water (less than 0.2%) to water twice as salty as the sea (7.0%). Nutrient (nitrogen and phosphorus) levels were high in the bay, and showed patterns of change from south to north. Nodularia spumigena was found in concentrations that greatly exceeded the World Health Organization’s standards for contact recreation. Laboratory studies suggest that nutrients and salinity are significantly correlated with levels of Nodularia spumigena from Farmington Bay. In combination with complex ecosystem interactions, nutrients and salinity in Farmington Bay apparently contribute to the high levels of Nodularia spumigena that we measured.