Phytoplankton populations are a primary driver of chemical and biological dynamics and are therefore important sentinel organisms for monitoring environmental perturbations. Additionally, long term ecological monitoring in the Potomac River estuary provides opportunities to examine phytoplankton dynamics. Annual blooms of the cyanoHAB Microcystis were observed in the 1970’s and 80’s, and since declined in frequency. A large Microcystis aeruginosa bloom occurred, summer 2011, prompting investigation of forecasting efforts for harmful algal species. Three prediction methods were investigated, with binary linear regression identified as the most appropriate forecasting tool. Coastal marine ecosystems are also at risk from climate change and phytoplankton provide a crucial monitoring tool. Extensive time series analysis revealed changes in phytoplankton phenology in response to climate indicators, mainly a shift in the timing of maximum abundance of diatoms and cryptophytes. It is likely that this change in phenology has an effect on energy transfer to higher trophic levels.