At Norje Sunnansund, an Early Holocene settlement in southern Sweden, the world’s earliest evidence of fermentation has been interpreted as a method of managing long-term and large-scale food surplus. While an advanced fishery is suggested by the number of recovered fish bones, until now it has not been possible to identify the origin of the fish, or whether and how their seasonal migration was exploited. We analysed strontium isotope ratios (87Sr/86Sr) in 16 cyprinid and 8 pike teeth, which were recovered at the site, both from within the fermentation pit and from different areas outside of it, by using laser ablation multi-collector inductively coupled plasma mass spectrometry. Our investigation indicates three different regions of origin for the fish at the site. We find that the most commonly fermented fish, cyprinids (roach), were caught in the autumn during their seasonal migration from the Baltic Sea to the sheltered stream and lake next to the site. This is in contrast to the cyprinids from other areas of the site, which were caught when migrating from nearby estuaries and the Baltic Sea coast during late spring. The pikes from the fermentation pit were caught in the autumn as by-catch to the mainly targeted roach while moving from the nearby Baltic Sea coast. Lastly, the pikes from outside the fermentation pit were likely caught as they migrated from nearby waters in sedimentary bedrock areas to the south of the site, to spawn in early spring. Combined, these data suggest an advanced fishery with the ability to combine optimal use of seasonal fish abundance at different times of the year. Our results offer insights into the practice of delayed-return consumption patterns, provide a more complete view of the storage system used, and increase our understanding of Early Holocene sedentism among northern hunter-fisher-gatherers. By applying advanced strontium isotope analyses to archaeological material integrated into an ecological setting, we present a methodology that can be used elsewhere to enhance our understanding of the otherwise elusive indications of storage practices and fish exploitation patterns among ancient foraging societies.