Lake Nakaumi, located near the Sea of Japan, holds significant ecological value. A detailed understanding of its intra-annual environmental variations under the broader context of global climate change is a fundamental basis for effective environmental management and the sustainable use of ecological resources. However, current research on this subject remains limited. In this study, we investigated the macrozoobenthic communities of Lake Nakaumi using a multi-index assessment approach, taking into account the lake’s hydrological characteristics. This allowed us to evaluate seasonal environmental changes and identify potential ecological risks. Our findings reveal that the macrozoobenthic community structure exhibits marked seasonal variation. Diversity peaks during the winter and spring, while it declines notably in the summer and autumn. Spatial differences in diversity levels across different lake regions are primarily attributed to habitat fragmentation driven by varying hydrological conditions. Overall, Lake Nakaumi is subject to significant environmental stress, and seasonal hydrological dynamics can cause abrupt shifts in community composition, thereby undermining the resilience of its aquatic ecosystem.