With increasing global temperatures, it remains unclear, how seedling emergence and survival will be affected in highly dynamic ecosystems like salt marshes. Our study combines passive and active warming treatments with the natural inundation dynamics of salt marshes. We studied the effects of active soil and passive air warming (ambient temperature, + 1.5°C and + 3.0°C) on seedling numbers of different species in three salt marsh zones (pioneer zone, low marsh, and high marsh) and on seedling survival (lifespan), seedling diversity and species richness in two salt marsh zones (low marsh and high marsh) in situ. We found a significant influence of warming on Shannon diversity at two dates, but we found no significant effects of warming on seedling number and survival. However, we found trends, which differed between zones. In the pioneer zone, seedling numbers were slightly higher in the warming treatments than in the ambient treatment from April to June. Whereas, in the high marsh, seedling numbers decreased more in the warming treatments during the same period. The median lifespan was slightly reduced under warming treatments. We conclude warming might have increased drought stress for seedlings in the high marsh, which led to the trend of lower seedling numbers and shorter survival times. Seedling number decreased with elevation, which could be attributed to both species‐specific strategies and differences in available space. Median survival differed significantly between species, which we assume is due to differing life‐history traits like seed size and if the species are annual or perennial.