Multispecies fisheries pose a considerable management difficulty with respect to quota allocation between species. The applicability is to single vessel and its individual quotas, as well as to the fleet as a whole. Negative externalities may be created if Total Allowable Catches (TACs) are not set in optimal proportions. That includes creation of unbalanced predator-prey relationships in the environment. This paper aims to develop a methodological framework for assessing the composition and distribution of TACs within heterogeneous fleet in a multispecies interaction system. The model is based on the individual technical efficiency dependent upon the vessel characteristics and associated flexibility with respect to utilizing quotas throughout the year. An empirical application is provided for the Polish Baltic Sea fleet, where the most valuable target species is cod. Multispecies interactions are incorporated as separate submodels for cod, herring, and sprat species, which are linked through predation. The regulatory body sets the annual quota based on the target fishing mortality varying between scenarios. The net present value of the fishery in each scenario is compared by simulating stock changes over time and paired with stock collapse probability estimates.