Coastal estuaries provide essential juvenile habitat for many commercially and recreationally important fish, which may move between estuarine and coastal environments throughout their life. Identifying the most important estuarine nurseries that contribute to the broader stock can support targeted management of juvenile and spawning populations. The objective of this study was to (1) compare chemical fingerprints within sagittal otoliths of juvenile Mulloway (Argyrosomus japonicus) sampled from putative south-eastern Australian nurseries, (2) assess their potential as natural tags to distinguish nursery grounds for the broader coastal Mulloway stock and (3) assess the viability of otolith chemistry as a fisheries management tool when limited to opportunistic, fisheries-dependant, otolith sample collection from by-catch. Otoliths from juvenile Mulloway (0 to 3 years, 4 to 44.8 cm total length) were obtained from 8 major estuaries and 2 inshore ocean locations along coastal south-eastern New South Wales, Australia, from April 2015 to July 2018. Concentrations of Sr, Ba, Mg, Mn and Li in the otolith region corresponding to the juvenile nursery stage were determined using laser ablation-inductively coupled plasma-mass spectrometry (LA-ICP-MS). The element to Ca ratios of fish from coastal estuaries differed significantly among collection areas, based upon multivariate elemental fingerprints, with some exceptions. When the otoliths of fish were analysed in a multinomial logistic regression (MLR) classifier, there was an overall mean allocation success of 59% to the estuary of capture. This study highlights the use of otolith ‘fingerprints’ as natural tags in Mulloway, and contributes to progressive research in environmental reconstruction applications of otolith chemistry.