Regime shifts in ecosystem structure and processes are typically studied from a temporal perspective. Yet, theory predicts that in large ecosystems with environmental gradients, shifts should start locally and gradually spread through space. Here we empirically document a spatially propagating shift in the trophic structure of a large aquatic ecosystem, from dominance of large predatory fish (perch, pike) to the small prey fish, the three-spined stickleback. Fish surveys in 486 shallow bays along the 1200 km western Baltic Sea coast during 1979–2017 show that the shift started in wave-exposed archipelago areas near the open sea, but gradually spread towards the wave-sheltered mainland coast. Ecosystem surveys in 32 bays in 2014 show that stickleback predation on juvenile predators (predator–prey reversal) generates a feedback mechanism that appears to reinforce the shift. In summary, managers must account for spatial heterogeneity and dispersal to better predict, detect and confront regime shifts within large ecosystems.