Elongated periods of low flow conditions, which can be termed as streamflow droughts, influence the nutrient (e.g., nitrogen and phosphorus) balance in estuarine systems. Analyzing temporal trends of nutrient fluxes into such systems under different streamflow regimes can complement the understanding about the dynamic evolution of streamflow droughts and their impacts on nutrient levels. The objective of this paper was to evaluate how dynamic evolution of streamflow droughts (from low flow conditions) affects the inorganic nutrient flux in a tropical estuarine system. We analyzed a 20-year time series of streamflow data together with the concentrations of two nutrient parameters—dissolved inorganic phosphorus (DIP) and dissolved inorganic nitrogen (DIN)—in the Lower Apalachicola River that drains into Apalachicola Bay in northeastern Gulf of Mexico, Florida. Our findings revealed that droughts affect the seasonal patterns and fluxes of both DIP and DIN. We also observed post-drought flushing patterns in DIP and contrasting changes in DIP and DIN fluxes in the long-term (20 years here) under different streamflow conditions. Dynamically changing correlations between the streamflow and the fluxes were found throughout different phases of droughts. In the long-term (from 2003 to 2021), the DIP flux in high flows increased by 35.3%, while the flux decreased by 15.7% in low flows. Conversely, DIN flux in high flows showed a decrease of <1.2%, but an increase of <23.7% in low flows after droughts end. The insights from this study highlighted the need for effective regulation plans such as proper nutrient management against streamflow droughts to mitigate negative ecological consequences in estuarine systems such as harmful algal blooms.