Phosphorus (P) loadings to the Great Lakes have been regulated for decades, but re-eutrophication and seasonal hypoxia have recently been increasingly reported. It is of paramount importance to better understand the fate, transformation, and biogeochemical cycling processes of different P species across the river-lake interface. We report here results on chemical speciation of P in the seasonally hypoxic Fox River-Green Bay system and variations in sources and partitioning of P species along the aquatic continuum. During midsummer when productivity is generally high, phosphate and dissolved organic P (DOP) were the major species in river water while particulate-organic-P predominated in open bay waters, showing a dynamic change in the chemical speciation of P along the river-bay transect with active transformations between inorganic and organic P and between colloidal and particulate phases. Colloidal organic P (COP, >1 kDa) comprised 33‒65% of the bulk DOP, while colloidal inorganic P was generally insignificant and undetectable especially in open bay water. Sources of COP changed from mainly allochthonous in the Fox River, having mostly smaller sized colloids (1–3 kDa) and a lower organic carbon to phosphorus (C/P) ratio, to predominantly autochthonous in open bay waters with larger sized colloids (>10 kDa) and a higher organic C/P ratio. The observed high apparent distribution coefficients (K_d) of P between dissolved and particulate phases and high-abundant autochthonous colloidal and particulate organic P in the hypereutrophic environment suggest that, in addition to phosphate, colloidal/particulate organic P may play a critical role in the biogeochemical cycling of P and the development of seasonal hypoxia.