Measurements of CH4 concentrations in the bottom water during two discrete sampling periods in subsequent years above different cold seeps at the Pacific margin off Costa Rica indicate large-scale variations of CH4 release. CH4 is emitted from mud extrusions and a slide scar at 1000–2300 m water depth. Maximum CH4 concentrations were found to be lower above all investigated sites in autumn 2003 than in autumn 2002 although seep sites are up to 300 km apart. Tidal and current changes were observed but found to apply only to individual seep sites. Increased seismic activity connected to the moment magnitude (MW) 6.4 earthquake offshore Costa Rica in June 2002 could have had an impact on all seep sites and thereby caused an increase in CH4 emission. This is supported by the largest variations of CH4 concentration found above mud extrusions located above faults likely more strongly affected by tectonic movements. Even though our data indicate a relation between seismicity and CH4 seepage, the relation is not proven, and future work is needed to comprehensively test this hypothesis.