The two subfamilies Hemerodromiinae and Clinocerinae, also known as aquatic dance flies, are a group of small predatory insects occurring mainly in mountainous areas and the northern temperate. However, very little is known about distribution patterns for most of the species. Habitat preferences for 40 aquatic empidid species were analysed in the Pieniny Mts., Poland. Forty-six sampling sites from a major part of this relatively low mountain massif (400-770m) were chosen, for which 17 micro and macrohabitat environmental variables were measured including both abiotic (altitude, stream mean width and depth, and shading) and biotic factors (13 dominant plant communities). Here we show that numerous studied aquatic Empididae were characterized by unique habitat preferences and were restricted to the foothills or the lower montane zone with only a few species characterized by wider elevational distribution. Chelifera pectinicauda, C. flavella, C. subangusta and Phyllodromia melanocephala (Hemerodromiinae), and Clinocera appendiculata, C. fontinalis, C. wesmaeli, Dolichocephala guttata, D. oblongoguttata, Kowarzia plectrum, Wiedemannia jazdzewskii, and W. thienemanni (Clinocerinae) were clearly associated with the highest altitudes and shaded areas while W. bistigma, W. lamellata, W. phantasma, and W. tricuspidata (Clinocerinae) were clearly associated with the lower elevated, wider stream valleys overgrown by willow brakes. Species richness and diversity decreased along elevational gradient with the hump-shaped diversity pattern noted for the subfamily Clinocerinae. The altitude, size of river/stream as well as the type of plant community were found as the most important factors in the distribution of the studied aquatic empidid species. The present study is the first one focused on elevational diversity gradient and habitat preferences of Hemerodromiinae and Clinocerinae of central Europe, and one of only a few in the world.