Several methanogenic pathways in oxic surface waters were recently discovered, but their relevance in the natural environment is still unknown. Our study examines distinct methane enrichments that repeatedly occur below the thermocline during the summer months in the central Baltic Sea. In agreement with previous studies in this region, we discovered differences in the methane distributions between the Western and Eastern Gotland Basin, pointing to in situ methane production below the thermocline in the latter (conc. CH 4 14.1 ± 6.1 nM, δ 13 C CH 4 −62.9 ‰). Through the use of a high resolution hydrographic model of the Baltic Sea, we showed that methane below the thermocline can be transported by upwelling events towards the sea surface thus contributing to the methane flux at the sea/air interface. To quantify zooplankton-associated methane production rates, we developed a sea-going methane stripping-oxidation line to determine methane release rates from copepods grazing on 14 C-labelled phytoplankton. We found that: (1) methane production increased with the number of copepods, (2) higher methane production rates were measured in incubations with Temora longicornis (125 ± 49 fmol methane copepod −1 d −1 ) than incubations with Acartia spp. (84 ± 19 fmol CH 4 copepod −1 d −1 ) dominated zooplankton communities, and (3) methane was only produced on a Rhodomonas sp. diet, but not on a cyanobacteria diet. Furthermore, copepod-specific methane production rates increased with incubation time. The latter finding suggests that methanogenic substrates for water-dwelling microbes are released by cell disruption during feeding, defecation, or diffusion from fecal pellets. In the field, particularly high methane concentrations coincided with stations showing a high abundance of DMSP-rich Dinophyceae. Lipid biomarkers extracted from phytoplankton- and copepod-rich samples revealed that Dinophyceae are a major food source of the T. longicornis dominated zooplankton community, supporting the proposed link between copepod grazing, DMSP release, and the buildup of subthermocline methane enrichments in the central Baltic Sea.