Soil phosphorus (P) built up due to past management practices, legacy P, in the Lake Okeechobee Watershed (LOW) in south-central Florida, U.S.A., is often discussed as the root cause of lake eutrophication. Improvement of the lake’s water quality requires the identification of critical P sources and quantifying their contributions. We performed a global sensitivity analysis of the Watershed Assessment Model (WAM), a common evaluation tool in LOW environmental planning, using the Morris method. A pre-calibrated WAM setup (Baseline) of the LOW sub-watershed, Taylor Creek Nubbin Slough (TCNS), was used as a test case. Eight scenarios were formulated to estimate the contributions of various P sources. The Morris analysis indicated that total phosphorus (TP) loads were highly sensitive to legacy P in improved pastures, the major land use covering 46.2% of TCNS. The scenario modeling revealed that legacy P, inorganic fertilizers, and other sources contribute 63%, 10%, and 32%, respectively, to the Baseline TP load of 111.3 metric tons/y to the lake. Improved pastures, dairies, citrus, and field crops are the top TP load contributors. Our results have important implications for water quality improvement plans in the LOW and highlighted the need for accurate spatial mapping of legacy P and incorporation of such information in modeling efforts for watersheds demonstrating legacy P problems.