Declines in predatory fish in combination with the impact of climate change and eutrophication have caused planktivores, including three-spined stickleback (Gasterosteus aculeatus), to increase dramatically in parts of the Baltic Sea. Resulting impacts of stickleback on coastal and offshore foodwebs have been observed, highlighting the need for increased knowledge on its population characteristics. In this article, we quantify abundance, biomass, size structure, and spatial distribution of stickleback using data from the Swedish and Finnish parts of the Baltic International Acoustic Survey (BIAS) during 2001–2014. Two alternative methods for biomass estimation suggest an increase in biomass of stickleback in the Baltic Proper, stable or increasing mean size over time, and larger individuals toward the north. The highest abundance was found in the central parts of the Baltic Proper and Bothnian Sea. The proportion of stickleback biomass in the total planktivore biomass increased from 4 to 10% in the Baltic Proper and averaged 6% of the total planktivore biomass in the Bothnian Sea. In some years, however, stickleback biomass has ranged from half to almost twice that of sprat (Sprattus sprattus) in both basins. Given the recent population expansion of stickleback and its potential role in the ecosystem, we recommend that stickleback should be considered in future monitoring programmes and in fisheries and environmental management of the Baltic Sea.