An unprecedented precipitation event in the hyper‐arid Atacama Desert of Northern Chile occurred in March 2015. Geomorphic alterations to the river channel and the coastal zone, coupled with the exceptional magnitude of the rainfall, caused catastrophic damage and loss of life. On the coast of the El Salado watershed, legacy mine tailings infilled the watershed‐ocean connection, while the river channel was altered both by tailings and urbanization. The consequences of this event resulted from the coupling of anthropogenic geomorphic changes with an unusual climate event. Lack of field data, complex geomorphology and sediment loads influenced by human activity make analysing floods in these regions especially challenging. The objective of this work is to improve our understanding of the factors that control flood hazards by using numerical simulations to reconstruct the 2015 flood in El Salado. We carry out unsteady two‐dimensional simulations fully coupled with the sediment concentration to identify the influence of tailing deposits, considering high‐resolution data of the pre‐ and post‐2015 flood topography. The results highlight the importance of specific event‐based studies, using models that can help designing better strategies for climate change adaptation and risk mitigation, while providing information for risk reduction and channel restoration.