Lake Nakaumi is a typical brackish lake located on the western coast of Honshu, Japan. The lake is dominated by phytoplankton, with a lack of higher aquatic organisms, resulting in relatively low ecosystem stability. The primary productivity of phytoplankton can be regarded as an important indicator of the current environmental status of Lake Nakaumi. Therefore, studying the dynamic changes in primary productivity is a crucial basis for implementing ecosystem management in the lake. In this study, this study used the mature Vertically Generalized Production Model (VGPM) and regression analysis to analyze the spatiotemporal variations of phytoplankton primary productivity (PPeu) in Lake Nakaumi from March 2023 to February 2024, as well as its main driving factors. This study explored the causes of differences in PPeu under different spatial and temporal conditions, summarized the key issues contributing to ecosystem instability, and identified sensitive periods and regions. Based on a comprehensive assessment, a systematic and feasible ecosystem management strategy for Lake Nakaumi is proposed.