Ocean climate change strongly affects organisms and ecosystems, and the causes, consequences, and underlying mechanisms need to be documented. In the Baltic Sea, a marginal sea under severe eutrophication stress, a longer productive season, and changes in the phytoplankton community over the last few decades have likely impacted diet and condition of keystone species, from individual to population level. This study uses stable isotopes (δ13C, δ15N, and derived isotope niche metrics) to trace energy and nutrient flows in archived samples of blue mussel (Mytilus edulis trossulus) spanning 24 yr (1993–2016). We test if long-term changes in isotope and elemental composition in mussels, as well as population abundance and biomass, can be explained by changes in abiotic and biotic variables, using partial least square regressions and structural equation modeling. We found decreasing trends in δ13C and δ15N as well as in mean size and total biomass of mussels, but no unidirectional changes in their stoichiometry or condition index. Changes in isotope composition were best explained by nitrogen-fixing cyanobacteria, by increased terrestrial organic carbon from land runoff (reflecting precipitation) and by decreases in dissolved inorganic nitrogen (indicative of successful eutrophication mitigation) and in biomass of a mixotrophic ciliate species. The trophic niche (assessed from isotope niche) was included as the best predictor for both mussel body condition and the observed decline in their total biomass.