Phytoplankton primary production (PP) in lakes play an important role in the global carbon cycle. However, monitoring the PP in lakes with traditional complicated and costly in situ sampling methods are impossible due to the large number of lakes worldwide (estimated to be 117 million lakes). In this study, bio-optical modelling and remote sensing data (Sentinel-3 Ocean and Land Colour Instrument) was combined to investigate the spatial and temporal variation of PP in four Baltic lakes during 2018. The model used has three input parameters: concentration of chlorophyll-a, the diffuse attenuation coefficient, and incident downwelling irradiance. The largest of our studied lakes, Võrtsjärv (270 km2), had the highest total yearly estimated production (61 Gg C y−1) compared to the smaller lakes Lubans (18 Gg C y−1) and Razna (7 Gg C y−1). However, the most productive was the smallest studied, Lake Burtnieks (40.2 km2); although the total yearly production was 13 Gg C y−1, the daily average areal production was 910 mg C m−2 d−1 in 2018. Even if lake size plays a significant role in the total PP of the lake, the abundance of small and medium-sized lakes would sum up to a significant contribution of carbon fixation. Our method is applicable to larger regions to monitor the spatial and temporal variability of lake PP.