Global climate change can affect the energy content of fish by altering their lipid physiology and lipid consumption. We investigated the effects of different environmental stressors on the lipid content of the Baltic herring (Clupea harengus membras) from spawning ground samples that were collected annually in the northern Baltic Sea. During 1987-2014, the average lipid content in herring muscle decreased from 5-6% (w.wt.) to 1.5% (w.wt.). Generalized linear mixed models (GLMMs) indicated that sea water salinity and the size of the herring stock explained best the declining trend of lipid content. We estimated that the amount of the lipid storage incorporated in the spawning stock decreased by approximately 45% during the study, with respective energy content decreases. Fatty acid composition analysis revealed that herring lipids contained a high proportion of EPA (20:5n-3) and DHA (22:6n-3), which originated from its main summertime prey, Limnocalanus macrurus. The results illustrate various climate change-induced processes leading to changes in the lipid content of the Baltic herring and, consequently, to changes in the energy flows of the northern Baltic ecosystem.