Surface sediments and three sediment cores from the western basin and one sediment core from the Sandusky basin were analyzed to document spatial and temporal changes in five phosphorus fractions and total phosphorus (TP). The areal distributions of the bioavailable fractions NaCl-Pi, NaBD-Pi, and NaOH-Pi and the refractory organic fraction Res-P were broadly consistent and contrasted with those of the detrital fraction HCl-Pi which showed that high concentrations occurred mostly in high-energy littoral zones and low concentrations largely in profundal depositional areas. The contrasting distributions were induced by interactions among tributary inputs, wave action, circulation, and biogeochemical cycling and transfer in the basin. As revealed by the Sandusky basin sediment record, the detrital fraction HCl-Pi was dominant (70% of TP) during European settlement and decreased rapidly by 28.0% in the early 1910s due largely to impoundments of the Maumee and Sandusky Rivers. While HCl-Pi has ever since remained relatively constant, NaCl-Pi, NaBD-Pi, and NaOH-Pi increased significantly between 1950 and 1970 in the two basins. However, the post-regulation sediment records differed considerably among these coring sites. There was a marked increase of TP in two cores, corresponding to recent return of eutrophication and massive harmful algal blooms but contrasting with a relatively constant, low loading into the lake. This signified the role of internal loading as derived partialy from legacy pollution. Furthermore, NaCl-Pi has increased progressively throughout all the records. We conclude that the increased levels of NaCl-Pi in surface sediments may have altered the internal loading and contributed to the resurgences of harmful algal blooms in Lake Erie.