The coastal marine protected ecosystem at Punta Coles (as a part of the Reserva Nacional de Islas, Islotes y Puntas Guaneras) is located in a highly exploited area in southern Peru and contains several commercial, bioengineering and other benthic species. Pre‐image population analysis was used to estimate the transient values of intrinsic growth rate (r) based on biomass and density time series as a proxy of productivity to assess the effectiveness of protection. The outcomes obtained showed that the gastropods Concholepas concholepas, Fissurella latimartiginata and the tunicate Purya chilensis showed a reduction of productivity during recent years, whilst the sea urchin Loxechinus albus, the barnacle Balanus laevis and the bivalve Semimytilus algosus showed an opposite pattern. Several species exhibited a chaotic dynamic, coinciding with the highest productivity values. In 2016 and 2017, several species exhibited a reduction of their abundance which could be delayed responses explained by changes in oceanographic conditions (reduction of coastal upwelling), La Niña event and illegal harvest. The above notwithstanding, the results suggest that effective protection of benthic species in the protected ecosystem of Punta Coles have been partially accomplished. Therefore, this work could be considered a baseline study, permitting the subsequent monitoring of productivity of the main species inhabiting the coastal area of Punta Coles. Pre‐image population analysis could be used as a complimentary analytical tool since it enables the evaluation of transient population parameters (e.g. productivity) thus aiding population management, conservation and monitoring decisions.