Abstract Methane (CH 4) concentrations were investigated in shelf waters of the north-eastern shelf of the Gulf of Cádiz (SW Iberian Peninsula) during four campaigns that took place in June 2006, November 2006, February 2007 and May 2007. CH 4 saturations, ranging from 70 to 1820%, showed great spatial and temporal variabilities. In general, strong onshore–offshore CH 4 gradients indicated an important coastal input, which was further supported by punctual data collected within the Guadalquivir and Guadalete estuaries, as well as in Rio San Pedro creek. Tidal exchange and enhanced freshwater inputs during rainy periods were found to be important factors controlling CH 4 distribution in shelf waters. The sediment was potentially another considerable source of biogenic CH 4 to bottom waters. CH 4 concentrations were found to be significantly higher in June and November 2006 compared to February and May 2007. The annual air–sea flux was estimated to range from 4.7 to 8.4 µmol CH 4 m − 2 d − 1 .