Marine ecosystems are exposed to increasing human pressures and climatic change worldwide. It has therefore become essential to describe ecosystem statuses with respect to multinational protection schemes, often necessitating long-term monitoring programmes. Changes in the food-web structure, which can be monitored via stable isotope measurements, represent an important descriptor of the status of marine ecosystems. We investigated long-term changes (29 years) in isotopic values (δ13C and δ15N) in four indicative organisms at different trophic levels in the southern North and Baltic Seas: bladderwrack (Fucus vesiculosus), blue mussel (Mytilus ssp.), eelpout (Zoarces viviparus), and herring gull (Larus argentatus). Time series analyses using generalised additive models revealed largely consistent declines in δ13C and δ15N throughout all trophic levels of the coastal food web at all study sites, indicating a clear change in these coastal regions from 1988 to 2016. There were no clear long-term patterns in egg biometrics for herring gulls, except for a consistent increase in eggshell thickness. The declines in stable isotope values were in line with the results of previous long-term studies of single higher-trophic-level species, which suggested that the noted changes were mainly caused by altered foraging patterns of the studied species. The current results demonstrate that declines in δ13C and δ15N have occurred throughout the whole food web, not just in particular species. We discuss the possible reasons for the decrease in stable isotope values, including decreasing eutrophication and an increase in terrestrial carbon sources.