The physiological challenges incurred during the transition from sea to fresh water and the constraints they place on the rate at which the common galaxiid Galaxias maculatus and the climbing galaxiid Galaxias brevipinnis can migrate from marine to freshwater habitats were examined. The duration of the marine to freshwater transition, the relationship between post-settlement age (PSA) and standard length (L(S)) as a proxy for energetic costs incurred during settlement and the potential effects of estuary geomorphology on migratory behaviour was investigated. Rate of upstream migration after settlement was not uniform. Upstream migration rate was slowest directly after settlement and increased with increasing PSA and distance from the river mouth, indicating a delay in upstream migration by newly recruited galaxiids. L(s) did not increase with age, at least within the first 21 days post settlement. These patterns were consistent for both species, in spite of differences in their life histories, across the recruitment season, despite seasonal variation in recruit size, and among estuaries with different properties. The results suggest that the timing and speed of migratory behaviour primarily reflect physiological constraints. Given the duration of residency of these species in estuaries, this study indicates that estuaries are critical transitional habitats for diadromous fishes during their migration from marine to freshwater habitats.