In many areas of the Baltic Sea, three-spined stickleback (Gasterosteus aculeatus) has increased several fold since the early 2000s. Two major planktivores of the Baltic Sea, Atlantic herring (Clupea harengus) and European sprat (Sprattus sprattus), may interact with stickleback via competition for food and predation, but the potential implications at the population level are still unknown. Here, we explored interactions between stickleback, herring, and sprat using (i) herring diet analyses and (ii) fish biomass estimates from hydroacoustics for 2001–2019 covering the largest Baltic Sea basins—the Central Baltic and the Bothnian Sea. The diet analyses revealed that stickleback is an important prey for large herring along the Swedish Baltic Sea coast, comprising up to 64% of the diet of individuals >22 cm. We found a negative influence of large herring (>18 cm) on stickleback in the Central Baltic, and a negative relationship between sprat and small herring (<18 cm) (pooled) and stickleback in the Bothnian Sea. The decline in herring and sprat population after the mid-1990s could have contributed to the increase in stickleback population via reduced predation and competition. Overall, herring may be an underappreciated piscivore, and high fishing pressure on herring could generate cascading effects on lower trophic levels.