Continental inland saline wetlands are among the most endangered habitats in Europe. In the Danube-Tisza-Danube canal network (Serbia, Southeastern Europe), which is one of the largest canal networks on the continent, the rare and endangered inland saline wetland Bolboschoenus maritimus community (BMC) has been found at only two locations. Two vegetation types of the community have been identified: (i) with Bolboschoenus maritimus and Marsilea quadrifolia (BMC-M) dominance and (ii) with Bolboschoenus maritimus and Butomus umbellatus (BMC-B) dominance. The aim of the study was to compare the habitats of the ascertained vegetation types in terms of 55 water and soil properties that influence their development, floristic composition and differentiation. The main properties influencing the community development and differentiation were water alkalinity, chemical oxygen demand, CO32−, water pH, soil conductivity, K+ and Ca2+ content in the soil. Both vegetation types grow in non-saline, slightly alkaline, nutrient-rich habitats with eutrophic water. When compared to BMC-B, BMC-M was found on heavy clay soils with higher conductivity, CaCO3, humus, nutrients, macroelements, and Na+ content, in shallower water with higher suspended solids and oxygen content, lower contents of nutrients, dissolved salts, HCO3−, macroelements, conductivity, and alkalinity. The study provides new data on the BMC distribution in this part of Europe and the first detailed information on its habitat conditions. Thirty-one species from the European Red List of Threatened Species were found in the stands. These results may be useful when deciding on the appropriate preservation measures aimed to rehabilitate other wetland habitats and biodiversity.