Understanding environmental predictor variables of species occurrence may contribute to conservation management. In this paper we test the use of a spatial binomial model, estimated with the combined INLA-SPDE method, to relate the probability of occurrence of the mussel Mytilus edulis in the subtidal part of the western Dutch Wadden Sea in the period 1992–2022, to a range of environmental and human-impact related variables. Salinity and orbital velocity appeared to be the most important driving variables, and maximum probability of occurrence was predicted at intermediate salinity levels around 22 PSU and low orbital velocity. Mussel occurrence was also lower in the shipping lanes that are regularly dredged. One of the hypotheses is that at lower salinity physiological stress occurs, but that at higher salinity levels predation limits the occurrence. The spatial structure of the unexplained variation is described by a Gaussian field, but it remained unclear what the type of underlying explanatory mechanisms could have been that some areas had much lower probability of occurrence than expected on the basis of environmental conditions. Further understanding of these observed patterns, for example by including temporal dynamics or experimentally testing settlement limitations, could benefit future decision making for conservation management.