Neobiotic species can have profound impacts on food webs and entire ecosystems. The American razor clam Ensis leei was introduced into the Wadden Sea by vessels in the late 1970s and has since spread widely. It has been suggested that Ensis does not interact strongly with other benthic species. The abundance and biomass of E. leei were recorded in 2393 samples in the north-eastern Wadden Sea and 800 samples in the south-eastern Wadden Sea over a total period of 9 years. Using an interdisciplinary approach, we developed a habitat prediction model using sedimentological and hydrodynamic predictors to help understand the shape of the ecological niche occupied by Ensis in the Wadden Sea. Our model showed that Ensis preferred areas with moderately high bed shear stress and prolonged or constant water coverage. Ensis preferred coarse sediments in the northern sub-area but coarse and muddy sediments in the southern sub-area and was negatively affected by the sand mason worm Lanice conchilega in the northern sub-area. Predictions of the spatial distribution of Ensis using the northern and southern datasets revealed major differences in predicted hot-spots throughout the entire study site. This study thus highlights the need to collect a sufficiently large dataset from different sub-areas of the Wadden Sea to allow valid conclusions to be drawn regarding the spatial distribution of Ensis. The negative effects of L. conchilega on Ensis abundance and biomass as well as the occurrence of Ensis in muddy sediments in the south suggest that the ecological niche of this neobiotic species is likely to overlap partly with the native fauna of the Wadden Sea. •Long-term data were used to determine ecological niche and predict habitat potential of Ensis leei.•Abundance and biomass of Ensis were related with sedimentologic and hydrodanamic predictors.•Ensis occurred both, in coarse sediments as well as in muddy environments.•Ensis abundance and biomass declined in areas with dense Lanice conchilega reefs.•The invasive Ensis is thought to overlap with the pristine benthic fauna particularly in muddy sediments.