Microphytobenthos (MPBs) are the main primary producers in shallow marine ecosystems, such as the Wadden Sea. We investigated the spatial and temporal dynamics of MPB communities across the marine-terrestrial boundary over three seasons (spring, summer, and fall) on three East Frisian Islands (Norderney, Spiekeroog, and Wangerooge) in the German Wadden Sea. Natural transects were compared with 12 experimental islands (salt marsh vegetated vs. initially bare islands) established on the tidal flats of Spiekeroog for studying dispersal-mediated community assembly. Sediment cores were taken along triplicate transects and on three elevation levels of the experimental islands, corresponding to the pioneer (pio) zone, the lower salt (LS) marsh, and the upper salt (US) marsh. On both the natural transects and the experimental islands, the highest MPB biomass was observed in the pio zone, where vegetation-driven sediment stabilization and high-mud content could have promoted MPB biomass in this marine-terrestrial transition zone. On the experimental islands, MPB biomass and diversity significantly decreased with elevation regardless of the season, indicating that the rarely submerged upper salt marsh level supported minimal MPB growth. The MPB biomass was also higher on initially vegetated than on bare islands, which was the most pronounced on the US level. On the tidal flat transects, the MPB biomass significantly increased with elevation up to the pio zone before decreasing again in the LS marsh. Temperature, sediment water content, and grain size significantly affected transect MPB biomass. MPB diversity, on the other hand, was not related to elevation but was rather determined by temperature, mean grain size, and mud content. Our study suggests that extending MPB studies into the “terrestrial” domain of salt marshes enhances our understanding of the microalgae–plant interaction in this important boundary zone.