Based on the analysis of multispectral satellite data, this work demonstrates the influence of coastal upwelling on the variability of chlorophyll-a (Chl-a) concentration in the south-eastern Baltic (SEB) Sea and in the Curonian Lagoon. The analysis of sea surface temperature (SST) data acquired by the Moderate Resolution Imaging Spectroradiometer (MODIS) onboard Aqua/Terra satellites, together with Chl-a maps from Medium Resolution Imaging Spectrometer (MERIS) onboard Envisat, shows a significant decrease of up to 40–50% in Chl-a concentration in the upwelling zone. This results from the offshore Ekman transport of more productive surface waters, which are replaced by cold and less-productive waters from deeper layers. Due to an active interaction between the Baltic Sea and the Curonian Lagoon which are connected through the Klaipeda Strait, coastal upwelling in the SEB also influences the hydrobiological conditions of the adjacent lagoon. During upwelling inflows, SST drops by approximately 2–8 °C, while Chl-a concentration becomes 2–4 times lower than in pre-upwelling conditions. The joint analysis of remotely sensed Chl-a and SST data reveals that the upwelling-driven reduction in Chl-a concentration leads to the temporary improvement of water quality in terms of Chl-a in the coastal zone and in the hyper-eutrophic Curonian Lagoon. This study demonstrates the benefits of multi-spectral satellite data for upscaling coastal processes and monitoring the environmental status of the Baltic Sea and its largest estuarine lagoon.