The dataset contains biogeochemical in situ field measurements taken in Batang Ai reservoir (located on the Borneo Island, Malaysia). Samples were taken over four sampling campaigns from 2016 to 2018. Data was used to analyse carbon dioxide and methane flux patterns and to calculate the carbon footprint of the reservoir in the paper: “The carbon footprint of a Malaysian tropical reservoir: measured versus modeled estimates highlight the underestimated key role of downstream processes” (https://doi.org/10.5194/bg-17-1-2020). Data were also used to calculate budgets of CO2 and CH4 in the epilimnion of Batang Ai reservoir in the paper: “Changing sources and processes sustaining surface CO2 and CH4 fluxes along a tropical river to reservoir system” (https://doi.org/10.5194/bg-2020-258).