Introductions of non-indigenous species (NIS) are mostly discussed through their impact on biodiversity. However, NIS can also act as ecosystem engineers, influencing the habitat itself, positively or negatively, directly or indirectly, which should be included when making risk assessments. Special concern should be given to changes in ecological services provided by the ecosystem. Physically, NIS may affect the substrate itself, or alter habitat architecture, indirectly influencing water movements, sediment accumulation, and light conditions. Chemical changes brought upon by NIS occur both on small and large scales, some having positive effects on ecosystem services, others can perturb epibionts. Furthermore, NIS may negatively affect natural resources, aquaculture or create fouling communities, all resulting in a negative impact on economics. However, if removed, already established NIS can be used as bioremediators, having a positive effect on different ecosystems. Using NIS for habitat management may be economically profitable, but could affect the habitat adversely.