Hypereutrophic estuaries are increasingly common features along global coastlines and are typically prone to micro- and macroalgal blooms, yet studies concurrently assessing the factors controlling these distinct algal populations in a single system have been rare. Jamaica Bay is an urban estuary that is hypereutrophic and experiences algal blooms that have been poorly characterized. During 2010 - 2012, the temporal and spatial dynamics of macro- and microalgal communities in Jamaica Bay were investigated in parallel with the factors that control the growth of these algal populations. Phytoplankton communities within the poorly flushed regions of Jamaica Bay (i.e. North Channel and Grassy Bay) reached extremely high densities during the spring and summer (> 135 ??g/L chlorophyll a; > 55,000 algal cells/mL) and were dominated by centric diatoms of the genera Thalassiosira spp.. The differences in the absolute magnitude of phytoplankton biomass across Jamaica Bay could be largely predicted from the residence time of water. Dissolved nitrogen (N) and phosphorus (P) concentrations were high throughout the year in Jamaica Bay while silicate (Si) concentrations were sometimes reduced to < 1??M and limited the growth of the dominant diatoms (Thalassiosira spp.) during the late spring and early summer. Such limitation facilitated a transition within the phytoplankton community toward autotrophic nanoflagellates. While often associated with excessive nutrient loading and poorly flushed water, dinoflagellates never dominated the algal community in Jamaica Bay. The macroalgal community in Jamaica Bay was dominated by the green alga, Ulva sp., with the densest populations (> 98% bottom coverage) present in the shallow, central portion of the bay and significantly lower coverage within deeper regions. The del-15N signature of Ulva tissue samples across most of the bay (13 - 17 ppt) indicated that waste water was the primary source of N for this alga and the N content of their tissues revealed that this alga was generally N replete. Accordingly, while nutrients almost never restricted the growth of Ulva, multiple lines of evidence indicated these populations were light limited within the deeper regions of Jamaica Bay. Finally, experimental incubations of phytoplankton and Ulva populations in Jamaica Bay indicated that phytoplankton can inhibit the growth of Ulva, likely via shading. Collectively, this study demonstrates that while phytoplankton communities in Jamaica Bay were largely controlled by flushing and Si, Ulva populations are controlled by light availability, which was largely controlled by phytoplankton communities.