Fish assemblages and their distributions in the western Balkan rivers have rarely been investigated. This study provides initial insights into the spatial patterns of fish distributions in the main-stem of the White Drin in Kosovo. Sampling primarily utilized back-pack electrofishing at 11 sites along the river's entire main stem, recording 21 species. Identification of most fish species was confirmed through DNA barcode analyses; two yet unnamed species are present and some taxonomic problems were discovered. The abundance of non-native species was low (5.9% of the catch) but seven of the eight non-natives have established populations. A longitudinal fish zonation pattern was described for the first time in this river; fish assemblages in an upstream-to-downstream gradient were characterized by a decrease of cold-water species (salmonids, minnows) and an increase of large-river cyprinids and non-native species. Multivariate ordination and network analyses demarcate preliminary fish assemblage types and specific environmental and anthropogenic pressure attributes are shown to influence assemblage structure. Natural assemblage patterns may be locally disrupted by anthropogenic pressures such as pollution and hydromorphological disturbances, however most sites show semi-natural features and conditions. Recommendations for conservation and further research are provided.