Due to its geographical position, relief features, specific geological past and great heterogeneity of space in a relatively small area, Bosnia and Herzegovina has specific hydro-morphological features, with numerous spring habitats and unique aquatic biodiversity, mainly composed by stenothermic and relict taxa. Spring habitats, as well as the flora and fauna that inhabit them are considered particularly vulnerable to climate change and anthropogenic pressures, due to their isolation and fragmentation. According to forecasts, these ecosystems will be exposed to multiple pressures caused by changes in water regime, rising water temperatures and a continuous decline in water quality, which will lead to the disappearance of more sensitive crenobiont species and a reduction in biodiversity. Therefore, in this chapter we present the ecological characteristics and specifics of spring habitats in Bosnia and Herzegovina, with a preliminary list of species that inhabit them and special focus on endemic, sensitive and rare species, which are potentially threatened by predicted changes in habitat quality.