The El Niño Southern Oscillation (ENSO) significantly influences marine ecosystems and the sustained exploitation of marine resources in the coastal zone of the Humboldt Current upwelling system. Both its warm (El Niño: EN) and cold (La Niña: LN) phase have drastic implications for the ecology, socio-economy and infrastructure along most of Pacific South America. Local artisanal fisheries, which especially suffer from the effects of EN, represent a major part for the domestic economy of Chile and Peru and in consequence a huge amount of published and unpublished studies exists aiming at identifying effects of EN and LN. However, most processes and underlying mechanisms fostering the ecology of organisms along Pacific South America have not been analyzed yet and for the marine realm most knowledge is traditionally based on rather descriptive approaches. We herein advocate that small-scale comparative and interdisciplinary process studies work as one possible solution to understand better the variability observed in EN/LN effects at local scale. We propose that differences in small-scale impacts of ENSO along the coast rather than the macro-ecological and oceanographic view are essential for the sustainable management of costal ecosystems and the livelihood of the people depending on it. Based on this, we summarize the conceptual approach from the EU-funded International Science and Technology Cooperation (INCO) project Climate variability and El Niño Southern Oscillation: Implications for Natural Coastal Resources and Management (CENSOR) that aims at enhancing the detection, compilation, and understanding of EN and LN effects on the coastal zone and its natural resources. We promote a multidisciplinary avenue within present international funding schemes, with the intention to bridge the traditional gap between basic and applied coastal research. The long-term aim is an increased mitigation of harm caused by EN as well as a better use of beneficial effects, with the possibility to improve the livelihood of human coastal populations along Pacific South America and taking differences between local socio-economic structures of the countries affected by EN into consideration. The success of such an approach however, does finally rely upon a willingness of the recourse users and the various political and economic stakeholders involved to taking on the message as part of sustainable management strategies.