Human impact often leads to reduced population sizes, and populations exposed to anthropogenic stress may suffer reduced evolutionary potential because of loss of adaptive genetic variation and higher risk of inbreeding depression (ID). Here, we exposed naive and carbaryl-selected inbred and outbred subpopulations of Daphnia magna to the pesticide carbaryl shortly after birth, and monitored acute (day 1–4) and post-exposure mortality (day 5—second clutch). Overall, acute mortality was lower than post-exposure mortality, indicating predominantly long-term costs of carbaryl exposure. Surprisingly, we found no indication for ID with respect to mortality upon carbaryl exposure. This may be due to more effective purging of deleterious alleles under standard conditions in the more homozygous inbreds as compared to the more heterozygous outbreds. Alternatively, homozygous pesticide resistance alleles in inbreds may render the inbreds an advantage compared to outbreds, where such resistance alleles would more likely occur heterozygotically. Additionally, we found that the capacity to further reduce mortality in response to carbaryl selection tended to be reduced in inbreds compared to outbreds. Our results thus suggest that inbred lineages may cope equally well as outbreds with pesticide stress.