This dissertation includes 3 chapters which focus on algal bloom of the tidal fresh James River. The first chapter describes nutrient and light limitation assays performed on algal cultures and draw conclusions about long-term patterns in nutrient limitation by comparing results with a previous study . This chapter also describes the influence of riverine discharge upon nutrient limitation in a point-source dominated estuary. This chapter was published in Estuaries and Coasts (Wood and Bukaveckas 2014). The second chapter presents the first comprehensive assessment of the occurrence of the cyanotoxin Microcystin in water and biota of the James River. Data presented in this chapter show that bivalve grazing declines in the presence of Microcystin in the water. The chapter also describes feeding habits in fish as a predictor for inter-specific differences in Microcystin accumulation in their tissues. The work presented in this chapter was published in Environmental Science & Technology (Wood et al. 2014). The third chapter describes the fate of algal carbon in the James River Estuary and the importance of autochthonous and allochthonous sources of organic matter in supporting production of higher trophic levels. Here I draw upon ecosystem metabolism data (NPP and R), abundance and grazing estimates for primary consumers and estimates of advective losses of chlorophyll and external inputs of nitrogen to place ‘top-down’ effects in the broader context of factors influencing chlorophyll and nitrogen fluxes in the James. . This chapter also describes results from mesocosm experiments used to assess the influences of grazers on chlorophyll, nutrients and Microcystis. This work will be submitted in the summer of 2014 to the journal Ecosystems.