Understanding marine ecosystem structure and functioning is crucial in supporting sustainable management of natural resources and monitoring the health of marine ecosystems. The current study utilized stable isotope (SI) mixing models and trophic position models to examine energy flow, trophic relationships, and benthic‐pelagic coupling between food web components. Roughly 1900 samples from different trophic levels in the food web, collected during 2001–2010 from four northern and central sub‐basins of the Baltic Sea, were analyzed for SI ratios of carbon and nitrogen. Trophic structure of the food webs among the sub‐basins was consistent, but there were differences between the proportions of energy in different trophic levels that had originated from the benthic habitat. Mysids and amphipods served as important links between the benthic and pelagic ecosystems. Much (35–65%) of their energy originated from the benthic zone but was transferred to higher trophic levels in the pelagic food web by consumption by herring (Clupea harengus). One percent to twenty‐four percent of the energy consumption of apex seal predators (Halichoerus grypus and Pusa hispida) and predatory fish (Salmo salar) was derived from benthic zone. Diets of mysids and amphipods differed, although some overlap in their dietary niches was observed. The food web in the Gulf of Finland was more influenced by the benthic subsystem than food webs in the other sub‐basins. The baseline levels of δ13C and δ15N differed between sub‐basins of the Baltic Sea, indicating differences in the input of organic matter and nutrients to each sub‐basin.