Eels (Anguilla spp.) are in decline worldwide, and the signs of reduced recruitment have been observed in continental Europe since the early 1970s. To aid recovery of the European eel, stocking is used by many European countries as a management option. In this study, tagging experiments were conducted to follow eel migration from Lake Mälaren and four sites along the Swedish east coast in the Baltic Sea. The recaptured tagged eels were retrieved from fishermen, allowing for the opportunity to investigate their origin (brackish water, stocked in freshwater or a mix in between) by otolith microchemistry and to assess for morphological differences after tagging. Several changes took place; for example, eye index increased while weight and condition decreased with migrated distance and time until recapture. In Lake Mälaren, the majority of tagged eels did not migrate out of the outlets, irrespective of their origin. Most of them were caught in the opposite direction and continued to be caught in the lake 1–3 years after tagging, with significant weight losses. Overall, overwintering is suggested to be an inferior option, but it is uncertain whether this is a natural behaviour or a result of translocation and restocking. For coastal eels, origin had no effect on migratory behaviour; a majority of the tagged eels migrated towards the outlet of the Baltic Sea. Interestingly, a minority of the recaptured eels originated from stocked fish. Instead, recaptures were dominated by natural immigrants that had spent most of their lives in brackish waters.