We estimated pelagic primary production (PP) in the coastal (< 200 m depth) Mediterranean Sea from satellite-borne data, its contribution to basin-scale carbon fixation, its variability and long-term trends during the period 2002–2016. Annual coastal PP was estimated at 0.041 Gt C, which approximately represents 12 % of total carbon fixation in the Mediterranean Sea. About 50 % of this production occurs in the eastern basin, whereas the western and Adriatic shelves contribute with 25 % each of total coastal production. Strong regional variability is revealed, from high-production areas (> 300 g C m−2) associated with major river discharges, to less productive provinces (< 50 g C m−2) located in the southeastern Mediterranean. PP variability in the Mediterranean Sea is dominated by interannual variations but overall trend during the study period shows notable decrease (17 %) since 2012 concurring with a period of increasing sea surface temperatures in the Mediterranean Sea and positive North Atlantic Oscillation and the Mediterranean Oscillation climate indices. PP declines in most coastal areas (−0.05 to −0.1 g C m−2 per decade) except in the Adriatic where PP increases at +0.1 g C m−2 per decade. Regionalization of coastal waters based on PP seasonal patterns reveals the importance of river effluents in determining PP in coastal waters that can regionally increase in up to five-fold. Our study provides insight on the contribution of coastal waters to basin scale carbon balances in the Mediterranean Sea while highlighting the importance of the different temporal and spatial scales of variability.