This study investigated how nitrogen and dissolved organic matter (DOM) from stormwater runoff and rainfall support the growth of Karenia brevis and Pyrodinium bahamense. Excitation–emission matrix spectroscopy coupled with parallel factor analysis tracked changes in the optical properties of DOM in each bioassay, revealing greater reactivity of terrestrial humic-like DOM. Significant increases in cell yield and specific growth rates were observed upon additions of runoff for both species, with significant increases in specific growth rates upon the addition of a 2 in simulated rain event for P. bahamense only. By hour 48, 100% of the dissolved organic nitrogen (DON) in each treatment was utilized by P. bahamense, and by hour 72, over 50% of the DON was utilized by K. brevis. The percentage of bioavailable dissolved organic carbon (DOC) was greater for P. bahamense compared to K. brevis, suggesting a greater affinity for DOC compounds by P. bahamense. However, the bioavailability of DOM for each species could be owed to distinct chemical characteristics of labile DOM conveyed from each site. This study demonstrates that stormwater runoff and rainfall are both sources of labile DOM and DON for K. brevis and P. bahamense, which has implications for blooms of these species in Tampa Bay waters.