When one wild species is food for another and both have their hunting enthusiasts, then conflict can arise. This is particularly true and complicated in fishing, where trophic links are strongly influenced by body-size ratios, alternative prey are available, populations are strongly density dependent and all their parameters are hard to quantify. We examine this problem with a specific example of trout-pike interaction in Irish lakes using a multi-species size-structured population model, set within a quantitative management action assessment framework. We use an informal Bayesian uncertainty analysis to account for empirical imprecision and test a range of stakeholder suggested scenarios for management of the pike and trout fisheries, under three different hypotheses about the abundance of non-trout prey availability. Trout fishing always diminished adult trout biomass. Fishing for pike always increased trout biomass but less effectively as biomasses of alternative (to trout) prey increased. Adult pike cannibalism was found to significantly alleviate predation pressure on trout when alternative prey was not plentiful, less so when it was.