Florida Bay, a shallow, seagrass-dominated bay in southern Florida, USA, receives significant nutrient inputs and has experienced seagrass losses and microalgal blooms within the last several decades. Inorganic nutrient inputs have been well characterized, but the role of organic nutri- ents, specifically of dissolved organic nitrogen (DON) and organic phosphorus (DOP), in supporting microbial processes in the bay is unknown. In this study various techniques were used to assess the importance of these nutrients along a transect in Florida Bay when a cyanobacterial bloom occurred in the central region in November 2002. These techniques included measurements of ambient particu- late and dissolved nutrients, enzyme (urease and alkaline phosphatase) activities, and experiments to determine rates of 15 N uptake (nitrate, ammonium, urea, and amino acids over a period of 0.5 h) and long-term (48 h) changes in microbial biomass and 15 N natural abundance in enrichment bioassays. The cyanobacterial bloom in central Florida Bay was associated with the highest concentrations of DON and DOP, whereas the microflagellate- and diatom-dominated eastern bay region was associ- ated with the highest concentrations of inorganic nutrients. The zeaxanthin:chlorophyll a ratio (an indicator of the relative contribution of cyanobacteria to phytoplankton biomass) was positively corre- lated with the rate of uptake of urea, and negatively correlated with the rate of uptake of inorganic nitrogen. The opposite pattern was observed for the fucoxanthin:chlorophyll a ratio (indicative of relative diatom biomass) and the peridinin:chlorophyll a ratio (indicative of relative photosynthetic dinoflagellate biomass), suggesting that different algal groups were using different N substrates. Bio- mass responses in the bioassay experiments showed that phytoplankton (as chlorophyll a) responded to DON additions in the western region and to DOP additions in the eastern region, but heterotrophic bacteria, in contrast, responded to DOP additions in the west and DON additions in the east. These findings thus demonstrate the potential for different sources of N, including DON, to stimulate differ- ent components of the algal community, and for the phytoplankton and bacteria to respond differently to N and P.