The goal of this two-year study was to explore the role of nutrients and climatic conditions in promoting reoccurring Alexandrium fundyense blooms in the Northport-Huntington Bay complex, NY, USA. A bloom in 2007 was short and small (3 weeks, 103 cells L?1 maximal density) compared to 2008 when the A. fundyense bloom, which persisted for 6 weeks, achieved cell densities >106 cells L?1 and water column saxitoxin concentrations >2.4 × 104 pmol STX eq. L?1. During the 2008 bloom, both deployed mussels (used as indicator species) and wild soft shell clams became highly toxic (1400 and 600 ?g STX eq./100 g shellfish tissue, respectively) resulting in the closure of shellfish beds. The densities of benthic A. fundyense cysts at the onset of this bloom were four orders of magnitude lower than levels needed to account for observed cell densities, indicating in situ growth of vegetative cells was responsible for elevated bloom densities. Experimental enrichment of bloom water with nitrogenous compounds, particularly ammonium, significantly increased A. fundyense densities and particulate saxitoxin concentrations relative to unamended control treatments. The ?15N signatures (1223) of particulate organic matter (POM) during blooms were similar to those of sewage (1030) and both toxin and A. fundyense densities were significantly correlated with POM ?15N (p < 0.001). These findings suggest A. fundyense growth was supported by a source of wastewater such as the sewage treatment plant which discharges into Northport Harbor. Warmer than average atmospheric temperatures in the late winter and spring of 2008 and a cooler May contributed to an extended period of water column temperatures optimal for A. fundyense growth (1220 °C), and thus may have also contributed toward the larger and longer bloom in 2008. Together this evidence suggests sewage-derived N loading and above average spring temperatures can promote intense and toxic A. fundyense blooms in estuaries.