Micro-estuaries are small, permanent water bodies periodically tidally connected to the ocean. There is limited knowledge regarding the ecology of micro-estuaries, and in particular, fish. This study aimed to investigate the fish assemblage, use and movement within two micro-estuaries in South Australia using traditional netting and imaging sonar techniques. A total of 13,667 fish were caught, with 14 species from 10 families identified, the most dominant being Atherinosoma microstoma, Aldrichetta forsteri, Pseudaphritis urvillii, and Pseudogobius olorum. Four estuarine functional guilds were found, with marine estuarine opportunists and marine stragglers the most dominant. Species richness (S = 11) and abundance (N = 6,035) where highest in summer compared to winter (S = 7, N = 522). The Multibeam Imaging Sonar used to assess fish movement observed 16,175 fish with a mean total length of 16.1 ± 4.6 cm. The number of fish per hour and biomass (kg/hr) was greatest at the mouth of the estuaries compared to upstream sites. Different life-history stages of both marine and estuarine-associated fish were found to use the micro-estuaries. Further research is required to understand these unique estuarine systems and evaluate ecological benefits from the restoration of micro-estuaries.