Oceanographically based mechanisms are shown to explain the spatial variation in the climatic relationship between the abundance of medusae (Aurelia aurita and Cyanea spp. of the class Scyphozoa), in the North Sea between 1971 and 1986 during June–August, and the winter (December–March) North Atlantic Oscillation Index (NAOI). A scyphomedusa population to the west of Denmark shows a strong inverse relationship between medusa abundance and fluctuations in the NAOI; the NAOI correlates strongly (P < 0.001) with both annual sea surface temperature (SST) at 6.5°E 56.5°N (1950–2008) and with winter precipitation on the Danish coast at Nordby (1900–2008) suggesting a direct link between the influence of climate and medusae abundance. In contrast, scyphomedusa abundance and distribution in the northern North Sea appears to be influenced by oceanic and mixed water inflow, which may overwhelm or mask any direct climatic influence on jellyfish abundance. Similarly, advection can also explain much of the interannual variability (1959–2000) in the abundance of other gelatinous zooplankton taxa (Cnidaria, Ctenophora and Siphonophora) in the northern North Sea as identified by the capture of gelatinous tissue and nematocysts (stinging cells) in Continuous Plankton Recorder samples. Jellyfish (Scyphozoa) in the southern North Sea may benefit from low temperature anomalies and the long-term effects of global warming might suppress Aurelia aurita and Cyanea spp. populations there. However, the biological response to temperature is complex and future research is required in this area.