Otolith chemistry has been widely used as a natural tag for determining environmental histories of fish that migrate across large distances and environmental gradients. However, it is not as well established as to whether otolith chemistry can be a useful tool for determining fine-scale movement and dispersal patterns of fish, particularly larvae, within estuaries. In this study, we collected water samples and otoliths from larvae of black bream, Acanthopagrus butcheri, an estuarine resident fish, and analyzed each for a suite of trace elements to determine the degree of spatio-temporal variability in elemental composition and which elements were incorporated into otoliths in relation to their associated water chemistry. We found that there were three distinct water layer signatures based on their Me : Ca_water (Me = each element): a freshwater signature, a halocline signature, and a marine signature. There were also significant spatio-temporal patterns in Me : Ca_otolith, most notably for Li : Ca, K : Ca, and Mn : Ca. This study provides encouraging evidence for the utility of intra-estuary otolith chemistry to reconstruct environmental histories during larval development. This application will enable a better understanding of the abundance, timing, and duration of residency in particular water masses and locations that are important larval nursery habitats for species that develop within estuaries.