Watershed fluxes of suspended sediment (SS), nutrients, in particular phosphorus (P), and cyanobacteria may play a role in driving cyanobacterial blooms along the southwestern shore of oligotrophic Lake Superior. To understand how tributary loads contribute to nearshore blooms, we sampled two southwestern shore tributaries, Bois Brule and Siskiwit Rivers. We collected water-quality samples to compute nutrient and sediment loads and to assess cyanobacteria community composition from the tributaries to the nearshore. We collected suspended and streambed sediment to assess the capacity for sediment to store and transport bioavailable P and to assess cyanobacteria community composition. Storm flows drove export of SS, total P, and total nitrogen, with the majority of total P being particulate P. Equilibrium P concentrations revealed that SS sorbed P as it is moved through the stream network across sites and seasons and was a potential source of P to the nearshore. However, streambed sediment in the Bois Brule and Siskiwit River watersheds were P sinks during summer, which potentially delayed transport of dissolved P to the lake. The cyanobacteria community varied spatially and temporally relating to multiple environmental variables including nutrients (P, N, and C) and specific conductivity. Cyanobacteria capable of producing cyanotoxins were present in tributaries and found across multiple environmental compartments indicating a potential for fluvial flow to the nearshore. This study demonstrated that streamflow is a primary driver of total nutrient and sediment loading in both watersheds, which indicates the potential for algal loading to the nearshore via suspended sediment or water.