Lake Lochloosa, Florida (USA) recently underwent a shift from macrophyte to phytoplankton dominance, offering us the opportunity to use a whole-basin, mass-balance approach to investigate the influence of phosphorus loading on ecosystem change in a shallow, sub-tropical lake. We analyzed total phosphorus (TP) sedimentation in the basin to improve our understanding of the forcing factor responsible for the recent shift to phytoplankton dominance. We measured 210Pb activity, organic matter (OM), organic carbon (OC) and TP in short sediment cores from 20 locations to develop a comprehensive, whole-basin estimate of recent mass sedimentation rates (MSR) for bulk sediment, OM, OC and TP. The whole-basin sedimentation models provided insights into historic lake processes that were not evident from the limited, historic water quality data. We used Akaike’s Information Criteria to differentiate statistically between constant MSR and exponentially increasing MSR. An eightfold, exponential increase in TP accumulation over the past century provided evidence for the critical role of increased P loading as a forcing factor in the recent shift to phytoplankton dominance. Model results show increased TP retention and decreased TP residence time were in-lake responses to increased TP loading and the shift from macrophyte to phytoplankton dominance in Lake Lochloosa. Comparison of TP loading with TP retention and historic, diatom-inferred limnetic TP concentrations identified the TP loading threshold that was exceeded to trigger the shift to phytoplankton dominance.