Abstract It is well known that the early life cycle stages of fishes are highly sensitive to chemical exposure. However, little is known about the effects of pollutants on the other life stages, due the difficulty of experimental/empirical approaches. Here we developed an experiment to evaluate the embryo-larval survival rate of the silver catfish (Rhamdia quelen) exposed to different source of pollution: untreated sewage, sewage treated by UASB technology and by recycling water technology (with and without chlorine). We then propose a stochastic individual-based model (IBM) to evaluate the effect of the pollutants on population dynamics of the species using four hypothetical scenarios where the pollutants affect: (I) only the embryo-larval stage; (II) both the embryo-larval and juvenile stages; (III) both the larval and adult stages; (IV) all three stages. Experimental approaches show high mortality rates, except the sewage treated by water recycling technology without chlorine. The theoretical model predicts that the adult population is not affected when the pressure of the pollutants is limited to the embryo-larval stage or both the embryo-larval and juvenile stages. However, a small decrease in adult survival probability (when the third and fourth scenarios are considered) can lead to a reduction in population size. When the pollutant affects proportionally all stages, the population reduces to 46% (UASB treatment) or become extinct (untreated sewage and recycling water treatment with chlorine). The recycling water treatment without chlorine shows to be the best treatment, reducing the population only to 80%. Our study highlights that it is necessary to improve the sewage treatment, otherwise it can promote harsh conditions for the biota accelerating the conditions that cause local extinction.