Headwater springs in the German Low Mountain Ranges are local ecotone habitats and biogeographical islands embedded in and interlinked with their adjacent landscape. The structure of forests reflects the eco-hydrological conditions in substrate type occurrence, microhabitat richness and biodiversity in forest springs. This study considers effects from different forest land cover by comparing spring habitats in deciduous beech forests and coniferous spruce forests on eco-hydrological structures and biodiversity. Study areas include six different forest landscapes in the Low Mountain Ranges in Central Germany in Hesse and Thuringia. Hydro-morphological structure mapping and invertebrate sampling was executed within a multi-habitat sampling regime, which involves sampling plots being allocated according to the cover ratio of the occurring substrata. Aquatic and terrestrial spring zones are considered with respect to an ecotone approach. Some in situ measurements were implemented, such as pH values, to assess the acidity of the spring water. Results show obvious differences in acidity, substrate type cover ratios and biodiversity in deciduous and coniferous forest springs. Conifer forest springs were found tending to acidification while deciduous forest springs were slightly alkaline. Deciduous forest springs had higher cover ratios of organic microhabitats as well as a higher biodiversity in species richness and total number of individuals. Although it was not possible to clearly distinguish one direct key factor of fauna assemblages, negative effects from forest management practices (e.g. monoculture plantations of conifer forest) on spring habitats can be concluded.