Estuarine recruitment of fishes is a potential bottleneck in the life cycle of many coastal species. We investigated patterns of size-at-ingress for larval and post-larval California halibut entering the Punta Banda Estuary (PBE), Mexico, using both otolith geochemistry and carbon stable isotope ratios (SIR). Juvenile halibut (n = 126; 38–163 mm standard length [SL]) were collected from inside PBE and the adjacent exposed coast during the fall of 2003, and otoliths (geochemistry) and muscle tissues (SIR) were analyzed to reconstruct the environmental histories of individuals. Based on geochemical analyses, nearly all fish collected from PBE were characterized by a non-estuarine signature (e.g., low Mn and Ba) in the otolith growth bands deposited when fish were <30 mm SL. Although fish collected from the coast retained that signature throughout their lives, fish collected within PBE showed elevated concentrations of Mn and Ba in the otolith growth bands deposited once halibut were 30–70 mm SL, thereby recording ingress. Carbon SIR of juvenile halibut prey also differed between the estuary and coast. Muscle δ 13C values of halibut captured along the coast were consistent (ca.−15‰), while those captured in the estuary were variable and generally more enriched in 13C (−16‰ to −11‰). Both natural tagging approaches agreed that most halibut (~75 %) enter PBE long after settlement (> > 8–12 mm SL), although size-at-ingress estimates were significantly larger (mean difference = 27 mm; p < 0.001) when derived via carbon SIR than with otolith geochemistry. Potential explanations for the differences in size-at-ingress estimates involve the magnitude of isotopic and trace element gradients at this ocean–estuary boundary, the temporal resolution of environmental tags stored within otoliths and soft tissues, and the size-at-capture or somatic growth rate of juvenile halibut. We conclude by discussing the relative merits of otolith geochemistry and SIR as natural tags, and by considering the implications of secondary dispersal into estuaries by post-larval fish.