Climate change and overfishing may lead to ecosystem instability and may benefit nonexploited organisms such as jellyfish. In the Irish Sea, an increase in jellyfish abundance was evident (r2=0.29, P=0.03) in a 16-year time-series (1994–2009) collected during juvenile fish surveys. Jellyfish abundance correlated positively with sea surface temperature (SST) over the preceding 18 months (r=0.65, pACF<0.001) and copepod biomass in the previous year (r=0.56, pACF=0.03) and negatively with spring (February–May) precipitation (r=−0.57, pACF=0.02). Principal components regression indicated that climatic indices explained 68% of the interannual variability in jellyfish abundance (P=0.003), where the components were based on the North Atlantic Oscillation Index, SST and precipitation. The frequency of cnidarian material present in Continuous Plankton Recorder (CPR) samples has also increased since 1970, with a period of frequent outbreaks between 1982 and 1991. Before this period, the herring stock in the northern Irish Sea declined rapidly to a low level, potentially stimulating structural change in the ecosystem. In 1985, there was a step decrease in CPR copepod biomass and in 1989, a step increase in the phytoplankton colour index, suggesting a cascading regime shift during the 1980s. Subsequent overexploitation of gadids, coupled with warm temperatures and the poor recruitment of cod, led to the rapid decline in cod biomass from 1990. While the biomass of sprat has decreased in the last decade, the herring stock has recovered partially. Reductions in demersal fishing pressure since 2000, intended to stimulate cod recovery, appear to have facilitated further rises in haddock biomass. Since the 1980s regime shift, sea temperatures have increased, the fish community has altered and jellyfish abundance has risen such that jellyfish and haddock may now play an increasingly important role in the ecosystem.