Benthic and planktonic sources of algae have distinct structural and functional attributes that exhibit unique ecological roles in river ecosystems dynamics. Hence, partitioning the contribution of benthic and planktonic sources to fluxes of algal biomass (chlorophyll-a) under different scenarios will help understanding ecosystem patterns of algal production and transport in river systems. Here, we combine concentration-discharge (C-Q) relationships of suspended chlorophyll during high-flow events, algal taxonomy, and river metabolism rates to characterize the origin, mobilization (proximal or distant sources), and contribution (mass-balance) of benthic and planktonic algae to primary production and biomass fluxes in different streams and rivers. Our study includes 7 sites from 5 different watersheds across the Delaware River Basin (DRB) ranging in size from 141km2 to 17,818km2 with varying structural complexity, land use, and nutrient concentrations. We show positive HI (0.199 ± 0.042) and positive FI (0.492 ± 0.051) values in three watersheds, indicating nearby sources that mobilize rapidly. In contrast, the Brandywine River (865km2), characterized by numerous low-head dams and lower nutrient concentrations, exhibits a negative HI (-0.187 ± 0.0295) indicating delayed mobilization of benthic algae. Interestingly, C-Q responses observed in the free-flowing portion of the Delaware River (17,818km2) significantly resemble those of much smaller watersheds, suggesting similar algal dynamics despite their channel size differences. Results from algal community composition show strong evidence of a clear separation between benthic and planktonic communities in <5th order streams but not at larger river systems. Regardless of watershed size, seasonal chlorophyll mass balances indicate that benthic supply is not sufficient to account for the observed chlorophyll fluxes, and that planktonic and off-channel sources are relevant to explain river exports of algae.