Seasonal seismicity in Japan has been observed and attributed to variations induced by hydrological loading, as well as atmospheric and pore‐fluid pressure. We examine the seasonal variations of crustal (<15 km depth) and low magnitude (M < 4.5) earthquakes in central Japan near the Biwako‐Seigan Fault Zone (BSFZ), and analyze their correlation with the annual hydrological cycle of nearby Lake Biwa, the largest freshwater lake in Japan. The 2002–2018 lake water storage is estimated using water‐level gauge and satellite altimetry data. Regional surface mass loading from soil moisture and snow predicted by the Global Land Data Assimilation System is used to augment the lake mass variation. We compute the stress and stressing‐rate changes induced by the surface mass loading from lake storage, snow, and soil moisture at seismogenic depth (10 km) along the BSFZ using a finite element model incorporating a 3D Earth structure. The results show that seasonal surface mass loading generates 1–5 kPa peak‐to‐peak Coulomb stress change and 2.5–15 kPa/year stressing‐rate variations on the fault segments along the BSFZ. Two of the four fault segments present significant correlation between local seismicity rate and loading‐derived stress and/or stressing rate changes. Among the hydrological load components, lake water, snow, and soil moisture exhibit different annual phases, and the lake water storage dominates the total annual stress changes. Our analysis indicates that seasonal surface hydrological loads, especially lake water variations, modulate the seismicity rate along the BSFZ in central Japan.