The macrobenthic community in shallow soft-bottom areas in the Bay of Ancón, Peru, is characterized by low biodiversity due to low oxygen concentrations. During El Niño (EN) events, higher water temperature and higher concentrations of dissolved oxygen induce a temporary increase in biodiversity. However, the structure and dynamics of the emerging macrobenthic community and populations, especially the polychaete Sigambra bassi, vary strongly among events. The reasons for this variation are poorly understood, in particular the relative influence of abiotic versus biotic factors. To disentangle how abiotic and biotic factors influence the different responses of the population of S. bassi, population models were developed based on detailed long-term monitoring data, which include four El Niño events. The results show that S. bassi abundances are favored by abiotic environmental conditions during EN, namely high temperature and dissolved oxygen concentration, but these abiotic effects are modulated by different biotic processes. In two EN events with relatively similarly high temperature anomalies (EN 1982-1983 and 1997-1998) different biological interactions (competition, predation, facilitation) and different species composition of the community resulted in different responses of the population of S. bassi.