Anthropogenic developments in coastal watersheds cause significant ecological changes to estuaries. Since estuaries respond to inputs on relatively long time scales, robust analyses of long-term data should be employed to account for seasonality, internal cycling, and climatological cycles. This study characterizes the water quality of a highly managed coastal basin, the St. Lucie Estuary Basin, FL, USA, from 1999 to 2019 to detect spatiotemporal differences in the estuary’s water quality and its tributaries. The estuary is artificially connected to Lake Okeechobee, so it receives fresh water from an external basin. Monthly water samples collected from November 1999 to October 2019 were assessed using principal component analysis, correlation analysis, and the Seasonal Kendall trend test. Nitrogen, phosphorus, color, total suspended solids, and turbidity concentrations varied seasonally and spatially. Inflows from Lake Okeechobee were characterized by high turbidity, while higher phosphorus concentrations characterized inflows from tributaries within the basin. Differences among tributaries within the basin may be attributed to flow regimes (e.g., significant releases vs. steady flow) and land use (e.g., pasture vs. row crops). Decreasing trends for orthophosphate, total phosphorus, and color and increasing trends for dissolved oxygen were found over the long term. Decreases in nutrient concentrations over time could be due to local mitigation efforts. Understanding the differences in water quality between the tributaries of the St. Lucie Estuary is essential for the overall water quality management of the estuary.