A long-term low nitrogen to phosphorus (N:P) ratio in the Tampa Bay, Florida, estuary system suggests that nitrogen is more limiting than phosphorus. However, south Florida suffered from a drought around 2007, and the reduction in runoff flowing into the bay affected local ecosystem dynamics. This study presents a remote sensing study to retrieve spatiotemporal patterns of total nitrogen (TN) concentrations in Tampa Bay under drought impacts through the integration of Moderate Resolution Imaging Spectroradiometer (MODIS) images and a genetic programming (GP) model. Research findings show that the drought impact on TN in Tampa Bay is both a seasonal and yearly phenomenon. Without the presence of ocean water intrusion, the whole bay would show a relatively uniform TN distribution during the drought period until the flow input from rivers returned to normal. Based on yearly comparisons, temperature could be the limiting factor on the plankton growth in Tampa Bay. To further substantiate the credibility of a nutrient estimation algorithm, a k-means clustering analysis was conducted to demonstrate sea-bay-land interactions among ebbs, tides, and river discharges. The seasonal cluster distribution in 2007 is generally consistent with the conventional segments division of Tampa Bay.