A time series analysis of long-term climate variability in northern Chile (18°21′-24°00′S) shows anomalies associated with the El Niño events and the longer warm period observed since 1976, followed by a cooling trend since mid 1980s. The succession of pelagic fisheries, anchovy (Engraulis ringens) and sardine (Sardinops sagax), occurring in this fishing zone was analyzed taking into account the landings, the CPUE abundance index, the fishing effort, and the environmental variables. The anchovy production model is a negative linear function of fishing effort and turbulence. For sardine, the production model is a negative linear function of fishing effort and a quadratic function of the sea surface temperature. An analysis of the relationship between recruitment, adult biomass and the environment shows that the annual recruitment of anchovy increases with turbulence intensity until wind speed reaches a value of 5.46 m s-1, decreasing for higher values. For sardine, the recruitment increases with turbulence intensity until 5.63 m s-1, stabilizing thereafter. It is deduced that the climatic variations associated to the El Niño events affect the abundance of coastal pelagic fishes, without forgetting the most likely effects upon its distribution and the fishing effort. However, it is the long-term variability that mainly affects the fishing activity.