Low-current tributary-estuaries and embayments along the margin of the Hudson River are uniquely at risk for harmful algal blooms of cyanobacteria (cyanoHABs) due to rising temperatures as a result of climate change. An increased prevalence of cyanoHABs in near-shore, low-current sections of the Hudson River could be extremely harmful to nearby communities, aquatic organisms and wildlife. To address this increased risk, it is imperative to understand the current in-stream and upstream abiotic environmental controls (nutrients, water temperature, etc.) on the current background levels of cyanobacteria within the Hudson River. It is also important to understand how these controls and cyanobacterial populations vary spatially with relation to the higher risk, lower-flow sections along the margins of the Hudson River. Locations of tributary-estuaries of special concern within the Hudson Valley include Esopus Creek in Saugerties, Rondout Creek in Kingston, and Wappingers Creek in Wappingers, NY. Other locations of concern are embayments along the Hudson River such as Long Dock Park in Beacon, Port Ewen in Kingston and Norrie Point in Staatsburg, NY. Given the lower-flow nature of these sites, elevated surface water temperatures are likely a result of settled, striated layers from decreased current. These locations are also susceptible to growth of the invasive species Trapa natans or commonly known as the European water chestnut. High concentrations of nutrients like nitrogen and phosphorous within the water chestnut bloom and the captured sunlight from metabolic processes like photosynthesis can create an ideal microhabitat for harmful algae like cyanobacteria. The background levels of cyanobacteria in outflows of tributaries, and their lower-flow estuary extensions were observed alongside the water quality within the water chestnut blooms of these sites at varying depths. By studying the weekly changes in background abundance of cyanobacteria and their drivers occurring at contrasting locations along the Hudson River, it was found that the strongest controls included turbidity, temperature and levels of phosphorous. In locations of low turbidity and high surface water temperatures, the background levels of cyanobacteria were higher in these lower-flow areas than in areas with increased turbidity. Cyanobacteria was found in greater number within water chestnut blooms than in whole water samples outside the area of the bloom. High surface temperature and riverbed temperature also related to higher levels of cyanobacteria. Given the concluded information, it is apparent that invasive water chestnuts within lower-flow extensions of the Hudson River hold a greater threat than originally understood; creating an ideal habitat for potential cyanoHABs in the wake of climate change.