Given the ongoing decline of many species, it is important to perform multifactorial analyses of conservation status and to assess the effects of species extinction on ecosystem services. In this study, we used long-term surveys to assess the influence of habitat change, landscape alteration and invasive species on extinction risk of the native crayfish Austropotamobius pallipes. We reviewed the existing literature to assess which ecosystem services are threatened by local extinction of A. pallipes and replacement with alien crayfish. We sampled 196 streams and wetlands in northern Italy. Of these, 117 received multiple surveys over a 13-year period (2004-2017), thus allowing accurate measurement of extinction rate. Thirty-four percent of A. pallipes populations underwent extinction between 2004 and 2017. The occurrence of alien crayfish in the catchment basin and urban growth in the landscape surrounding streams were associated with A. pallipes extinction. The probability of persistence was significantly higher in populations close to stream springs and with physical barriers (especially waterfalls) separating them from basins with alien crayfish. Extinction of native crayfish alters community structure and impairs regulating services such as detrital breakdown and pest regulation. Replacement by alien crayfish (Procambarus clarkii and Faxonius limosus) also threatens supporting and regulating services by altering nutrient cycling, food webs, sediments and erosion. The implementation of management practices that control river connectivity using selective barriers is needed to prevent further local extinction of native species. Integrating information on extinction with knowledge of impacts on ecosystem services is essential in developing more effective conservation policies.