To identify lake properties and watershed environments regulating partial pressure of carbon dioxide (pCO2) at the surface water, a field survey was performed in summer for 77 lakes. These lakes were located at latitudes between 35 and 43 °N with altitudes from 5 to 2700 m in Japanese islands and differed largely with respect to trophic conditions, basin morphometries, and land use and land cover in the watersheds. Among the lakes, pCO2 in the surface water varied more than three orders of magnitude (1.4-1749.7 Pa) and was higher than that at atmospheric levels in 73% of the lakes, suggesting that the majority of the lakes were net heterotrophic. Among the within-lake variables, biomass of both zooplankton and phytoplankton as well as the sediment area of mixed layer were important predictors of pCO 2 at the surface. Thus, lake CO2 concentrations are regulated by the balance of autotrophic and heterotrophic activities, and sediment respiration is a crucial source of CO2 supersaturation, especially in shallow isothermal lakes. The best model for pCO2 at the lake surface water included relative size of deciduous forests, grasslands, and urban areas in the watershed. The balance of autotrophic and heterotrophic activities in lakes depends highly on land use and cover in the watershed. Changes in terrestrial vegetation can affect carbon metabolism, even if local anthropogenic activities in the watersheds are unchanged.