The problem of salt water intrusion into the Mekong Delta is a research topic involving various branches of science. Among the causes of this phenomenon are global sea level rise and regulation of the natural river discharge due to hydropower dam construction. The scale of the delta and its water dynamics complicate instrument-based observations. Meanwhile, communities of living organisms can serve as indicators of environmental heterogeneity. This study aimed to analyze the spatial variability of fish assemblage organisation in the Mekong Delta for use as an indicator of salt water intrusion. The composition of fish assemblages in different parts of the delta were determined by midwater trawl catches during January and April 2021. A total of ~15 thousand individual fish from 74 trawl hauls were captured and analyzed. The null hypothesis was that the fish assemblages in the Mekong Delta are represented by three taxonomic complexes that are localized in the upper course (freshwater), the lower course (brackish) and the middle course (zone of the contact of the fresh and brackish waters) of the delta. The taxonomic composition of the freshwater complex is the most poor and is represented by 9 families. Meanwhile, marginal (the contact zone) and brackish complexes include 26 and 23 families, respectively. Specimens of families Cobitidae, Eleotridae, Plotosidae and Siluridae that are only found in the zone of contact of fresh and brackish waters could be considered as indicator species of its position. The actual boundaries of the brackish and freshwater complexes were determined and the distance from them to the marine delta edge equals 34 and 78 km, respectively. Assessment of the salinity values that correspond to the complex boundaries is a task for future investigation. The position of the boundaries of freshwater and brackish fish taxonomic complexes has a biological basis and could be used as an indicator of salt water intrusion into the Mekong Delta.