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 51 % 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 in coastal PP, 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 a notable basin-scale decline (17 %) has been observed since 2012 concurring with a period of increasing sea surface temperatures in the Mediterranean Sea and positive North Atlantic Oscillation and Mediterranean Oscillation climate indices. Long-term trends in PP reveal slight 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 up to 5-fold. Our study provides insight into 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.