Salt marshes represent a unique ecosystem at the marine-terrestrial boundary of shallow protected coastlines. Microarthropods form an essential component of soil food webs, but how they colonize new intertidal habitats is little understood. By establishing two experimental systems without animals, we investigated microarthropod colonization (1) at the seashore from the pioneer zone to the lower and upper salt marsh and (2) at the same tidal height on artificial islands 500 m from the seashore. Potential source populations of microarthropods in the respective zones were also investigated. Colonization of microarthropods after 5 years was consistently faster on the seashore than on the artificial islands. Collembola and Mesostigmata colonized all the zones both on the seashore and on the artificial islands, with colonization being faster in the upper salt marsh and in the pioneer zone than in the lower salt marsh. Oribatida colonized the new habitats on the seashore, but only little on the artificial islands. Variations in species composition were more pronounced between salt marsh zones than between experimental systems, indicating that local environmental conditions (i.e., inundation frequency) are more important for the assembly of microarthropod communities than the distance from source populations (i.e., dispersal processes). Variations in community body size of Oribatida and Mesostigmata indicated environmental filtering of traits, with smaller species suffering from frequent inundations. Notably, Mesostigmata most successfully colonized the new habitats across salt marsh zones on both systems. Overall, the results document major mechanisms of colonization of intertidal habitats by microarthropods with different life histories and feeding strategies.