P>1. Transplant experiments with adult plants showed that marsh plant zonation along estuarine salinity gradients develops according to species tolerances of abiotic factors and biotic interactions. Thus, glycophytes are restricted from salt marshes by abiotic stress, whereas halophytes are excluded from freshwater marshes by competition. We hypothesized that adult plant zonations along estuarine stress gradients are predefined by processes affecting plants during their seedling phase. In an experimental glasshouse study, we tested how a mixed community of glycophytes and halophytes developed during the first months of early establishment affected by different flooding and salinity regimes. 2. We set up two factorial mesocosm experiments that tested the effects of three tidal regimes (daily tide, spring tide, no tide) and three salinity levels (fresh, brackish, salt) on the emergence and early establishment of glycophyte and halophyte seedlings. In the Emergence Experiment seedlings were identified and removed once per week. In the Establishment Experiment species cover was estimated every 2 weeks, and after 15 weeks final above-ground biomass of each species was determined. 3. Both glycophytes and halophytes showed highest seedling emergence under freshwater conditions. Emergence of halophytes was less impaired by increased salinities than that of glycophytes. Emergence and establishment of glycophytes were extremely reduced under brackish and salt conditions, whereas under freshwater conditions, glycophytes showed a consistent increase in cover over time. Cover of halophytes showed a similar increase in brackish and salt treatments; however, in freshwater treatments it significantly decreased after week 9. While daily tides predominantly decreased seedling emergence and establishment, spring tides had no significant effects on seedlings in freshwater and negative effects in saltwater treatments. 4. Synthesis. The ability of a species to germinate and emerge under conditions representing a particular position along an environmental gradient is necessary but not solely responsible for determining plant zonation patterns along estuarine marsh gradients. Our results show that competitive exclusion of halophytes by glycophytes as an important driver of marsh plant zonations along estuarine salinity gradients takes effect already during the early seedling establishment phase of the co-occurring plants.