Assemblages of juvenile fish and associated abiotic parameters were investigated inside and outside Jinju Bay in southern Korea, on a monthly basis from December 2014 to November 2015. Fluctuations in water temperature and salinity were larger inside than outside the bay. In total, 534,657 individuals per square kilometre from 81 fish species and 47 families were collected during the study period. The most dominant species was Nuchequula nuchalis both inside (25.6%) and outside (26.9%) the bay. The next dominant species were Thryssa kammalensis (17.9%) and Zoarces gillii (16.0%) inside the bay and Liparis tanakae (16.9%) and T. kammalensis (9.0%) outside the bay. Forty species (33% of total number of individuals) of young fish were recorded inside the bay and 47 species (52%) outside the bay. Therefore, it appears that a diversity of fish use nursery grounds inside and outside Jinju Bay. In particular, the following six species appeared: Z. gillii, Pleuronichthys cornutus, L. tanakae, Hemitripterus villosus, Pennahia argentata, and Xenocephalus elongates. Due to assemblage differences for fishes within Jinju Bay and outside the bay, management of both areas is required to maintain current diversity of species in the region.