We investigated the impact of viruses, nutrient loading, and microzooplankon grazing on phytoplankton communities in two New York estuaries that hosted blooms of the brown tide alga Aureococcus anophagefferens during 2000 and 2002. The absence of a bloom at one location during 2002 allowed for the fortuitous comparison of a bloom and non-bloom year at the same location as well as a comparison of two sites experiencing bloom and non-bloom conditions during the same year. During the study, blooms were found at locations with high levels of dissolved organic nitrogen and lower nitrate concentrations compared to a non-bloom location. Experimental additions of inorganic nitrogen and phosphorus yielded growth rates within the total phytoplankton community which significantly exceeded control treatments in 83% of experiments, while A. anophagefferens experienced significantly increased growth during only 20% of experimental inorganic nutrient additions. Consistent with prior research, these results suggest brown tides are not caused by eutrophication, but instead are more likely to occur when sources of labile DOM are readily available. Microzooplankton grazing rates on the total phytoplankton community during a bloom were lower than grazing rates at a non-bloom site, and grazing rates on A. anophagefferens were lower than grazing rates on the total community on some dates, suggesting that reduced grazing mortality may also promote brown tides. Mean densities of viruses during blooms (3 × 108 ml−1) were elevated compared to most estuarine environments and were twice the levels found at a non-bloom site. Experimental enrichment of the natural viral densities yielded a significant increase in A. anophagefferens growth rates relative to control treatments when background levels of viruses were low (<1.7 × 108 ml−1), suggesting that viruses may promote bloom occurrence by regenerating DOM or altering the composition of microbial communities.