<p>Poor bivalve growth in Kumihama Bay, a brackish lake in Kyoto, has raised concerns about nutrient dynamics. This study examined nutrient supply from hypoxic water masses during the cold season (October–May) and its role in phytoplankton blooms. Monthly observations (2023–2024) measured dissolved oxygen concentration (DO), chlorophyll-a fluorescence, pH, and nutrient concentrations. Long-term data (2007–2023) were analyzed for nutrient trends. In summer, decomposition in hypoxic waters accumulated dissolved inorganic nitrogen (DIN) and phosphorus (DIP). As the intrusion depth of oceanic water by estuarine circulation deepened from autumn to winter, these nutrients were transported upward by advection and diffusion, forming a subsurface chlorophyll maximum. In January, the breakdown of the hypoxic water mass coincided with the homogenization of nutrient concentrations across the bay, contributing to the continuation of the cold-season phytoplankton bloom, which culminated in its peak during the spring. Thereafter, nutrient concentrations in the upper layers gradually declined toward summer. Long-term data showed a significant decrease in total nitrogen (TN) and a reduction in nutrient inputs from terrestrial sources, suggesting a decline in both new and regenerated production. These findings indicate that nutrient loading from hypoxic water masses plays a crucial role in supporting primary production during the cold season. Furthermore, the long-term decline in this nutrient supply may negatively affect the bivalve feeding environment.</p>