The fish and tadpole assemblages inhabiting micro-estuaries and micro-outlets along a warm-temperate section of the Eastern Cape coast were investigated over four seasons between 2015 and 2016. The specific aim of this study was to elucidate whether nekton assemblages in coastal microsystems are similar to those found in larger estuarine systems on the same coastline, and whether the presence or absence of tadpoles can indicate a difference between the two microsystem types. Oligohaline and/or freshwater conditions prevailed in micro-outlets for much of the sampling period, while micro-estuaries were mostly mesohaline. Nekton communities in micro-outlets were dominated by tadpoles (Xenopus laevis), with juvenile Pseudomyxus capensis sometimes present, while Oreochromis mossambicus, Gilchristella aestuaria, P. capensis and Mugil cephalus were the most common fish species in micro-estuaries which had an almost complete absence of tadpoles. The micro-estuaries had a low estuarine function when compared to temporarily open/closed estuaries, while the micro-outlets had very limited estuarine characteristics and an almost complete absence of fishes. Due to their restricted periods of stability and small size, micro-estuaries served as only intermediate nursery areas for small numbers of 0+ marine fish which, after less than a year, need to migrate to nearby larger estuarine systems that can provide the full range of nursery habitats for subsequent growth and development. The limited numbers of estuarine resident fishes (e.g. G. aestuaria) and freshwater fish species (e.g. O. mossambicus) confirm the marginal habitat and food availability in these microsystems for fishes that are normally abundant in other types of Eastern Cape estuaries and rivers. The results of this study confirm that there are clear distinctions between the nekton of the two microsystem types, thus making fish and tadpole assemblages a viable tool for differentiating between micro-estuaries and micro-outlets in this province.