The eastern boundary of the Chile-Peru Current System constitutes one of the most biologically productive ecosystems in the world, due largely to coastal upwelling and the horizontal advection of nutrients. In this ecosystem, El Nino events are of great importance in the interannual variability of the environment. A change was observed in the environmental regime at the beginning of the 1970s with the onset of the 1972-1973 El Nino, marking an important decrease in the anchovy fishery (Engraulis ringens). After the mid-1970s, sardine (Sardinops sagax) landings increased noticeably. A second regime shift at the end of the 1980s was seen mostly in the noticeable recovery of anchovy and the decline of sardine. Herein, we present an integrated conceptual model of the different local and large-scale phenomena that affect the marine environment off northern Chile and the distribution and abundance of pelagic resources. The model considers an analysis of environmental and bio-fishery data on different scales and describes how the interdecadal (associated with regime shifts) and interannual (associated with El Nino events) fluctuations in the Equatorial Pacific are manifested in the eastern South Pacific and, therefore, in the northern zone off Chile, affecting the annual cycle, the dynamic of the coastal trapped waves, and coastal upwelling. In this framework, interdecadal fluctuations play an important role in the anchovy-sardine-anchovy replacement sequence.