There has been a widespread increase in the reporting of harmful and ‘nuisance’ algal blooms in the coastal ocean over the past few decades. On the global scale this is suspected to be a consequence of coastal eutrophication, however, on a case-by-case basis there is usually insufficient evidence to discriminate between the effects of human and natural causal factors. Intense blooms of the ‘Brown Tide’ unicellular algae (Aureococcus anophagefferens) have occurred sporadically since 1985 in coastal waters of Eastern Long Island and have devastated the local commercial scallop fishery. Analysis of an 11-year time-series dataset from this region indicates that bloom intensity is correlated with higher salinities and inversely correlated with the discharge of groundwater. Laboratory and field studies suggest that whereas salinity is unlikely to represent a direct physiological control on Brown Tide blooms, the addition of inorganic nitrogen tends to inhibit Brown Tide blooms. Budget calculations indicate that the inorganic nitrogen supply from groundwater is 1–2 orders of magnitude higher than any other external source of nitrogen for this ecosystem. Biweekly time series data collected in 1995 demonstrate that Brown Tide blooms utilize dissolved organic nitrogen (DON) for growth, as evidenced by a large decrease in DON parallel with an increase in cell abundance. On an interannual basis, bloom intensity was also positively correlated with mean DON concentrations. We hypothesize that bloom initiation is regulated by the relative supply of inorganic and organic nitrogen, determined to a large extent by temporal variability in groundwater flow. The 1980s and 1990s were characterized by exceptionally high and interannually variable groundwater discharge, associated with a large-scale climate shift over the North Atlantic. This, coupled with the time-lagged discharge of groundwater with high nitrate concentrations resulting from increased fertilizer use and population increase during the 1960s and 1970s, may have been a key factor in the initiation of Brown Tide blooms in 1985.