Springs are unique aquatic habitats that contribute significantly to local and regional biodiversity because of their high habitat complexity and the large number of different spring types. Many springs are small, but they are numerous and often of high water quality, and thus, provide habitats for species that are rare elsewhere because of their sensitivity to anthropogenic impacts (least-impaired habitat relicts). Springs are often species-rich and contain a larger number of Red List taxa than other aquatic habitats. Hydrological factors, particularly flow permanence, water chemistry, and temperature are important ecological factors determining species distribution and community composition. Despite their importance for biodiversity and water quality, springs are much less studied than other aquatic ecosystems. They also are insufficiently covered by protective legislation, often resulting in the destruction of their natural habitat. The authors of papers in this special issue describe specific spring biota, including multitaxon studies, and discuss the role of environmental factors, habitat variability at different spatial and temporal scales, and the importance of natural and anthropogenic disturbance in spring habitats. They suggest directions for future research, including defining reference conditions for springs and their role in long-term ecological research, the development of quality-assessment methods, and their more sustainable use as freshwater resources.