Stokell’s smelt has an unusually restricted distribution confined to several large rivers of the Canterbury coast on the South Island of New Zealand. Previous descriptions of its life history assumed that it spawns in estuarine zones of these rivers and the larvae or juveniles then migrate to sea, spending most of their life in coastal marine habitats before returning as adults to the estuary to breed. Several questions arise from these assumptions such as whether adults home to natal rivers and why the species is not more widespread if it spends its adult life at sea. The life histories of Stokell’s smelt from all the major rivers of the east coast of the South Island were investigated from patterns in the otolith microchemistry determined by laser ablation ICPMS. Fish from all rivers showed no evidence of prolonged marine residency as expected from ratios of strontium (high) and barium (low) to calcium in the otolith. Instead fish showed ratios consistent with long-term residency within the estuarine zone but with periodic changes indicating regular excursions into less saline waters. The remarkable periodicity of these movements is possibly associated with lunar tidal cycles. Variation in otolith microchemistry between populations fits with differences in estuary geomorphology. Stokell’s smelt appears to be an estuarine specialist that occupies the saline boundary in the major rivers where it occurs. Estuarine philopatry possibly explains the species’ restricted distribution and may result in significant genetic differentiation between river metapopulations. Individual populations may also be highly susceptible to any deterioration in the condition of their river such as alterations in flow regime or increasing nutrient and sediment loads.