Planning and license applications concerning groundwater diversion in areas containing water-dependent or water-favored habitats must take into account both hydrological effects and associated ecological consequences. There is at present no established methodology to assess such ecohydrological responses. Thus, this paper describes a new stepwise methodology to assess ecohydrological responses to groundwater diversion from, e.g., water-drained pits, shafts, tunnels, and caverns in rock below the groundwater table. The methodology is illustrated using the planned deep-rock repository for spent nuclear fuel at Forsmark in central Sweden as a case study, offering access to a unique hydrological and ecological dataset. The case study demonstrates that results of ecohydrological assessments can provide useful inputs to planning of monitoring programs and mitigation measures in infrastructure projects. As a result of the assessment, artificial water supply to wetlands is planned in order to preserve biological diversity, nature values, and vulnerable species.Electronic supplementary materialThe online version of this article (doi:10.1007/s13280-013-0404-8) contains supplementary material, which is available to authorized users.