<p>In 1997, dikes were constructed to isolate the inner section of Isahaya Bay from the Ariake Sea’s western coast, creating a freshwater reservoir. Following reclamation, the bay experienced an increase in red tides due to the frequent release of eutrophic, high-turbidity water from the reservoir, which contains significant amounts of labile organic nitrogen. Because most of the suspended matter in the drainage from the reservoir sinks near the dike, the particulate labile organic nitrogen introduced by the drainage may have accumulated in the surface sediment near the dike and promoted the regeneration of NH₄⁺-N from the sediment into the water column. In the present study, we found that amino acids, which are typical bioavailable organic nitrogen, accumulated near the dike and decreased with increasing distance. Thus, the accumulation of bioavailable organic nitrogen may have been caused by drainage from the reservoir. High NH₄⁺-N concentrations were also observed in pore water near the dike. The concentration of NH₄⁺-N showed a positive correlation with both the levels of amino acids and the freshness of organic matter, which was induced by the amino acid composition. These results indicated that the NH₄⁺-N concentration is controlled by the degree of accumulation of fresh and bioavailable organic nitrogen. The relatively high levels of NH₄⁺-N found in the bottom water could be partially attributed to the movement of NH₄⁺-N from the sediment into the overlying water, potentially serving as a significant nitrogen source for red tides near the dike in Isahaya Bay.</p>