Freshwater ecosystems are experiencing increased salinization. Adaptive management of harmful algal blooms (HABs) contribute to eutrophication/salinization interactions through the hydrologic transport of blooms to coastal environments. We examined how nutrients and salinity interact to affect growth, elemental composition, and cyanotoxin production/release in two common HAB genera. Microcystis aeruginosa (non-nitrogen (N)-fixer and microcystin-LR producer; MC-LR) and Aphanizomenon flos-aquae (N-fixer and cylindrospermopsin producer; CYN) were grown in N:phosphorus (N:P) 4 and 50 (by atom) for 21 and 33 days, respectively, then dosed with a salinity gradient (0 – 10.5 g L^-1). Both total MC-LR and CYN were correlated with particulate N. We found Microcystis MC-LR production and release was affected by salinity only in the N:P 50 treatment. However, Aphanizomenon CYN production and release was affected by salinity regardless of N availability. Our results highlight how cyanotoxin production and release across the freshwater – marine continuum are controlled by eco-physiological differences between N-acquisition traits.