Cordulegaster heros is an endemic species for Central and Southeastern Europe and one of the species protected under the European Union’s Habitats Directive. To adequately protect this species and its habitats, it is of crucial importance to have detailed information on its distribution, habitat requirements and potential threats to its survival. The main aims of this study were to record Cordulegaster heros geographical and altitudinal distribution and habitat requirements (stream width, fine substrate content and habitat shading), along with the importance of protected area network in its conservation and threats to its habitats in Croatia. To achieve those aims, we investigated 201 perennial and intermittent streams across three biogeographical regions (Continental, Alpine, Mediterranean). Additionally, in a small-scale study conducted in streams located within a protected area, we assessed the species’ relationship with water quality. According to the current results, Cordulegaster heros was confirmed to reproduce in 44 perennial streams in the Continental and Alpine regions, with a significantly higher number of sites and species’ abundance recorded in the Continental region. As the species was not recorded in the Mediterranean region, its occurrence there remains unverified. The species occurred at an altitudinal range between 150 and 665 m a.s.l., with 77% of the sites being between 150 and 350 m a.s.l. It was mostly documented in streams with widths up to 250 cm, fine sediment content up to 30%, and high habitat shading (>75%). A small-scale assessment of its relationship with water parameters within a protected area revealed a significant correlation with higher concentration of oxygen and lower conductivity, confirming its requirements for clean and well-oxygenated habitats. Approximately 57% of the sites where this species was recorded are within the protected area network. However, because most known occurrences are concentrated within only one area, the Continental region, along with the rather low population densities and anthropogenic threats (e.g., deforestation, hydro-morphological alterations) present at 43% of those streams, further monitoring activities are necessary. The presented results provide a basis for further monitoring of Cordulegaster heros and its habitats in Croatia.