We use six decades of catch-at-age data for perch (Perca fluviatilis) and pike (Esox lucius) in Windermere (UK) to estimate age- and sex-specific population sizes, natural mortalities and catchabilities in both species. Population sizes are estimated by fitting age structured population models to the catch-at-age data using standard maximum likelihood methods. We validate our methods using data simulations, and use our estimates of vital rates (natural mortality, recruitment and catahability) to address important aspects of fisheries biology. Our model indicates that strong fishery selection against male perch apparently triggered a population collapse, highlighting that sex-selective fisheries can be harmful even at a reasonable exploitation rate (here ≤30%). Recruitment (R) increased with the abundance of spawners (S) in both species, but it also responded to both abiotic and other biotic factors. In particular, increased predator (pike) abundance induced a change from compensation to depensation in the prey (perch) SR relationship, thus favouring the occurrence of an Allee effect. Our study provides reference points for the effective exploitation of pike and perch populations, and underscores the need for ecosystem-based harvesting management.