Food-web indicators for marine management are required to describe the functioning and structure of marine food-webs. In Europe, the Marine Strategy Framework Directive (MSFD), intended to lead to a ‘good environmental status’ of the marine waters, requires indicators of the status of the marine environment that also respond to manageable anthropogenic pressures. Identifying such relationships to pressures is particularly challenging for food-web indicators, as they need to be disentangled from linkages between indicators of different functional groups caused by species interactions. Still, such linkages have not been handled in the indicator development. Here we used multivariate autoregressive time series models to identify how fish indicators in an exploited food-web relate to fishing, climate and eutrophication, while accounting for the linkages between indicators caused by species interactions. We assembled 31-year long time series of indicators of key functional groups of fish in the Central Baltic Sea pelagic food-web, which is characterized by strong trophic links between cod (Gadus morhua) and its main fish prey sprat (Sprattus sprattus) and herring (Clupea harengus). These food-web indicators were either abundance-based indicators of key piscivores (cod) and zooplanktivores (sprat and herring) or size-based indicators of the corresponding trophic groups (biomass of large predatory fish (cod ≥ 38 cm) and biomass of small prey fish (sprat and herring