Information on movement patterns of marine fishes between estuarine populations and stocks at sea is fundamental to understanding their population dynamics, life history tactics and behavior. Furthermore, understanding estuarine habitat use by marine fishes is crucial for their effective conservation and integrated estuarine management. Although large numbers of young marine fish make use of temperate estuaries in highly predictable abundance patterns, very little is known about how estuarine populations interact with the populations at sea. Recruitment of sand goby Pomatoschistus minutus (Pallas, 1770) into the low salinity zone of the Scheldt estuary (Belgium) was reconstructed over an entire year by means of an isotopic clock. These results were combined with a growth model to yield age and length at immigration. Sand gobies entered the upper Scheldt estuary almost continuously from May onwards, except in July when they appeared to avoid the estuary due to warm summer temperatures. About 70% of the fish caught in the upper estuary resided there for less than 1 month, which indicates a strong temporal overlap of immigration and emigration. This complex migration pattern suggests that estuarine residence is caused by trade-offs made at the individual level, whereby migration is probably triggered by temperature. The high turnover of individuals in the estuarine population leads us to question the functional role of the estuary for marine fishes. Sand gobies entering the upper estuary had a wide range of ages and body sizes, although they were at least 2 months old and had a minimum standard length of approximately 20 mm. This study shows that the use of an isotopic clock strongly complements catch data and is useful to describe the connectivity between populations.