We identified different distributions of marine nonindigenous species (NIS) and native species on some artificial structures versus natural reefs and using experimental manipulations, revealed some possible causal mechanisms. In well-established subtidal assemblages, numbers of NIS were 1.5–2.5 times greater on pontoons or pilings than on rocky reefs, despite the local species pool of natives being up to 2.5 times greater than that of NIS. Conversely, on reefs and seawalls, numbers of native species were up to three times greater than numbers of NIS. Differential recruitment to different positions and types of surfaces appeared to influence distribution patterns. NIS recruited well to most surfaces, particularly concrete surfaces near the surface of the water, whilst natives occurred infrequently on wooden surfaces. The position of rocky reefs and seawalls close to the shore and to the seabed appeared to make them favourable for the recruitment of natives, but this positioning alone does not hinder the recruitment of NIS. We argue that pontoons and pilings represent beachheads (i.e. entry points for invasion) for many nonindigenous epibiota and so enhance the spread and establishment of NIS in estuaries. Habitat creation in estuaries may, therefore, be a serious threat to native biodiversity.