Since river metabolism often depends highly on site-specific environmental conditions, it is unsure if there are general trends in seasonality and latitudinal gradients. To uncover such uncertainties, we examined Gross Primary Productivity (GPP), Ecosystem Respiration (ER) and Net Ecosystem Productivity (NEP) in 16 rivers across Japan in spring (May), summer (August) and autumn (November) using the hourly data of dissolved oxygen and water temperature that were recorded from 2010 – 2016 by the river stations of Ministry of Land, Infrastructure and Transport. The selected river stations had latitudinal coordinates ranging from 42.93°N to 33.32°N and stream order ranging from 4 to 7. The metabolic rates were estimated by BAyesian Single-station Estimation Model (BASE v2.2) with additional data on Photosynthetically Active Radiation (PAR), atmospheric pressure and salinity recorded by Meteorological Agency at nearest sites to the river stations. The results showed that mean GPP for rivers was 2.78, 5.28 and 2.38 g O₂ m^-2 d^-1 and the mean ER was 4.93, 6.55 and 5.53 g O₂ m^-2 d^-1 in spring, summer and autumn, respectively. Most of the rivers examined were heterotrophic regardless of the seasons. With the statistical analyses, we compare and discuss the variation of NEP amongst different seasons and locations.