The Peru‐Humboldt Current system (HCS) supports the world's largest pelagic fisheries. Among the world's eastern boundary current systems, it is the most exposed to high climatic stress and is directly affected by El Niño and La Niña events. In this volatile ecosystem, fish have been led to develop adaptive strategies in space and time. In this paper, we attempt to understand the mechanisms underlying such strategies, focusing on the El Niño 1997–98 in Peru from which an extensive set of hydrographic, capture and acoustic survey data are available. An integrated analysis of the data is crucial, as each has substantial shortcomings individually; for example, both catch data and acoustic surveys may easily lead to wrong conclusions. Existing hypotheses on anchovy and sardine alternations lead us to a ‘habitat‐based’ synthetic hypothesis. Using our data, an integrated approach evaluated how fish responded to habitat variation, and determined the consequences in terms of fish‐population variability. Various factors occurring at a range of different spatio‐temporal scales were considered: interdecadal regime (warm ‘El Viejo’/cool ‘La Vieja’ decadal scale); strength and the duration of the El Niño Southern Oscillation event (interannual scale); population condition before the event (interannual scale); fishing pressure and other predation (annual scale); changes in reproductive behaviour (intra‐annual scale); presence of local upwelling (local scale). During El Niño 1997–98, anchovy was able to exploit a small‐scale temporal and spatial ‘loophole’ inside the general unfavourable conditions. Moreover, sardine did not do better than anchovy during this El Niño and was not able to take advantage of the ‘loophole’ opened by this short‐term event. Our results question the traditional view that El Niño is bad for anchovy and good for sardine.

[1] The near-coastal circulation of the Northern Humboldt Current System is described analyzing $8700 velocity profiles acquired by a shipboard acoustic Doppler current profiler (SADCP) during 21 surveys realized between 2008 and 2012 along the Peruvian coast. This data set permits observation of (i) part of the Peru Coastal Current and the Peru Oceanic Current that flow equatorward in near-surface layers close to the coast and farther than $150 km from the coast, respectively; (ii) the Peru-Chile Undercurrent (PCUC) flowing poleward in subsurface layers along the outer continental shelf and inner slope; (iii) the near-surfacing Equatorial Undercurrent renamed as Ecuador-Peru Coastal Current that feeds the PCUC; and (iv) a deep equatorward current, referred to as the Chile-Peru Deep Coastal Current, flowing below the PCUC. A focus in the PCUC core layer shows that this current exhibits typical velocities of 5-10 cm s À1 . The PCUC deepens with an increasing thickness poleward, consistent with the alongshore conservation of potential vorticity. The PCUC mass transport increases from $1.8 Sv at 5 S to a maximum value of $5.2 Sv at 15 S, partly explained by the Sverdrup balance. The PCUC experiences relatively weak seasonal variability and the confluence of eddy-like structures and coastal currents strongly complicates the circulation. The PCUC intensity is also affected by the southward propagation of coastally trapped waves, as revealed by a strong PCUC intensification in March 2010 coincident with the passage of a downwelling coastal wave associated with a weak El Niño event.

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Every 2–7 years, El Niño events trigger a strong decrease in phytoplankton productivity off Peru, which profoundly alters the environmental landscape and trophic chain of the marine ecosystem. Here we use a regional coupled physical‐biogeochemical model to study the dynamical processes involved in the productivity changes during El Nino, with a focus on the strongest events of the 1958–2008 period. Model evaluation using satellite and in situ observations shows that the model reproduces the surface and subsurface interannual physical and biogeochemical variability. During El Niño, the thermocline and nutricline deepen significantly during the passage of coastal‐trapped waves. While the upwelling‐favorable wind increases, the coastal upwelling is compensated by a shoreward geostrophic near‐surface current. The depth of upwelling source waters remains unchanged during El Niño but their nutrient content decreases dramatically, which, along with a mixed layer depth increase, impacts the phytoplankton growth. Offshore of the coastal zone, enhanced eddy‐induced subduction during El Niño plays a potentially important role in nutrient loss.

El Niño events, in particular the eastern Pacific type, have a tremendous impact on the marine ecosystem and climate conditions in the eastern South Pacific. During such events, the accumulation of anomalously warm waters along the coast favors intense rainfall. The upwelling of nutrient-replete waters is stopped and the marine ecosystem is strongly impacted. These events are generally associated with positive surface temperature anomalies in the central and eastern equatorial Pacific. During austral summer 2017, a strong surface temperature anomaly reaching ∼3-4 • C off Northern Peru and Ecuador led to intense coastal precipitations. However, neutral temperature anomalies were recorded in the equatorial Pacific. Using in situ measurements, satellite observations, and simulations from an eddy-resolving regional ocean circulation model, we investigated the physical processes triggering this peculiar 'coastal El Niño.' Its impact on the regional ocean circulation and heat budget off northern Peru and Ecuador was assessed. Using model sensitivity experiments, we investigated the respective roles of the equatorial Kelvin waves and local wind anomalies in driving the anomalously high nearshore sea surface temperature (SST). The atmospheric teleconnections which triggered the event were investigated using reanalysis data.