Water quality data from 1981 to 2015 were used to elucidate the spatiotemporal distributions of chlorophyll a (Chl.a) concentration and Secchi depth in the west-central Seto Inland Sea, Japan. The results revealed that salinity and distance from the northern coastline were the main factors for predicting Chl.a concentration and Secchi depth, respectively. Significant differences in both of these were observed between subareas in spring, summer and autumn; differences were insignificant in winter. Chl.a concentrations have decreased for the past 35 years, while their extent differed in the subareas. A greater rate of decrease in Chl.a concentration was observed in the innermost Hiroshima Bay in spring, compared with other subareas, while no significant difference in different subareas was found in other seasons. Secchi depth has increased for the past 35 years, but no significant difference in its rate of increase was found among different subareas in all seasons. Total nitrogen loading better explained changes in mean Chl.a concentration than total phosphorus throughout the west-central Seto Inland Sea. Phytoplankton's contributions to light attenuation were low in the west-central Seto Inland Sea, indicating that the nutrient loading reduction programme has been of limited effectiveness in improving water clarity.