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A functional trait-based approach is crucial for understanding ecosystem function, persistence, and protection. Vegetation in inland salt marsh habitats has been recognized as unique on a European scale and is legally protected under the Natura 2000 network. Despite long-term international protection, this continues to decline. The concept of inland salt marsh protection refers to vegetation in the sense of syntaxonomical units. However, no link has been found between syntaxonomical and functional concepts of vegetation. We aimed to identify functional traits that are distinctive to individual vegetation units and to link these traits to environmental factors. We hypothesized that a) syntaxonomical vegetation units are also functional units in terms of their functional traits, and b) environmental factors determine the functional traits of vegetation patches. We considered a set of traits from the CLO-PLA and LEDA databases responsible for the persistence, regeneration, and dispersability of approximately 400 species recorded in 874 plots classified into nine vegetation classes and five associations typical of salt marshes. We found that the syntaxonomical vegetation units were also functional. The most important factors separating vegetation classes and salt marsh plant associations are the functional traits responsible for plant persistence. The values of these traits were generally negatively correlated with soil salinity and positively correlated with soil moisture and abandonment of mowing or grazing. Traits related to regeneration, such as seed number and seed number per shoot, also play essential roles in grouping species into individual associations. The classes specific to salt marshes, Therosalicornietea and Festuco-Puccinelietea, had the lowest persistence potential and were thus the most sensitive to environmental changes. The most sensitive association seemed to be Salicornietum ramossissimae. Therefore, significant attention should be paid to protecting this vegetation type. Puccinellio distantis-Spergularietum salinae and Agrostio stoloniferae-Juncetum ranarii had significantly lower stability and higher regenerative ability. Therefore, their regeneration must be easier and more effective. Triglochino maritimae-Glaucetum maritimae and Scorzonero parviflorae-Juncetum gerardi associations had low regeneration ability. The functional pattern of the analyzed vegetation may play a crucial role in the effective protection and restoration of endangered natural saline habitats.