The Everglades Agricultural Area (EAA) in South Florida (USA) is a recognized source of total phosphorus (TP) that has impacted downstream oligotrophic Everglades marshes. Treatment wetlands, called stormwater treatment areas (STAs), were constructed and subsequently expanded to remediate EAA-derived TP, ideally yielding long-term outflow concentrations to the Everglades Protection Area (EvPA) of 13 µg/L TP or less. To date, TP-remediation has been insufficient relative to TP loads discharged from some EAA basins. We assessed 20 years of EAA basin-level and farm-level TP concentration and outflow data with the goal of understanding trends over time and identifying TP hot spots. Using monitoring data from water year (WY) 2000 through WY 2019, TP discharged from EAA farms averaged 74.68 ± 38.87 µg/L and was as high as 269.38 µg/L. We identified spatial and temporal variations in TP concentration, farm outflow, TP load, and TP flow-weighted mean concentration from the EAA farms. EAA basins TP concentration showed the presence of a decreasing trend between WY 2000 and WY 2012 and increasing trends for the more recent period WY 2010 to WY 2019. Using a nine-parameter Analytic Hierarchy Process (AHP), we observed that 31% of EAA farms posed above-average pollution risk, including 22 farms in the S-5A and 17 farms in the S-6 basins. These hot spot farms are primary candidate sites for targeted interventions aimed at reducing TP runoff, alleviating the TP burden on downstream STAs, and offsetting the recent increasing trend.