The freshwater Lakes IJsselmeer and Markermeer have undergone major shifts in abiotic and biotic conditions in recent decades. Strong reduction in productivity, hab-itat changes, and establishment of invasive species have altered the fish community and conditions for commer-cial fisheries. Fishery on perch (Perca fluviatilis), pike-perch (Sander lucioperca), bream (Abramis brama), roach (Rutilis rutilus), eel (Anguilla anguilla) and smelt (Osmerus eperlanus) has declined severely. New requirements related to implementation of European legislation regarding water quality (Water Framework Directive) nature conservation (Bird- and Habitat Directive) and Eel Regulation set further boundaries to fisheries activities. This stimulated the development of scientific advisory tools to support fisheries manage-ment including broader ecological aspects, such as food reservation for fish-eating birds and impact of migra-tion barriers on survival of silver eel. These aspects are generally captured well as different sources of mortality in population models, which give direct information on the effect of management measures. In addition, eco-logical risk assessments are used to facilitate manage-ment decisions.