Due to ongoing changes and a decline in biodiversity, science today should rely on long-term species-based ecological studies. We have conducted a long-term ecological dynamics study on the water beetle family Scirtidae, which, although it is very abundant in benthic communities, is still poorly studied. The main objective of this study was to investigate the population aspects (composition, diversity, sex ratio) and ecological aspects (emergence patterns, seasonal dynamics and preferences for environmental factors) of the family Scirtidae over 15 years in Plitvice Lakes NP, Croatia. The study was conducted at three sites and in five different substrate types. A total of three taxa with different distributions were recorded in the study area: Hydrocyphon novaki and H. deflexicollis on the tufa barriers and the Elodes sp. in the spring area. The sex ratio was in favour of males in spring and early summer, while it shifted in favour of females towards the end of autumn. The abundance and emergence of the family were primarily determined by the environmental parameters which showed the greatest fluctuations over a period of 15 years: water temperature, water discharge and oxygen saturation. Our results clearly show that Scirtidae can be used as indicators of stream zonation and habitat quality. Based on the methodology and the results of this study, we conclude that Scirtidae should be used in future monitoring and protection measures in karst freshwater habitats in southeastern Europe.