This study aimed to review habitat diversity and conservation value of small fluvial and gravel pit lakes along river-floodplain systems in the Western Balkans. Aquatic habitat types were presented according to the EU Habitats Directive and the Bern Convention, while the physical habitat properties were evaluated following the standard approach for hydromorphological assessment of lakes in Europe. Habitats considered as conservation priorities are present in both types of small water bodies, covering a wide range of water trophic gradient and hydromorphological conditions. This phenomenon, coupled with macrophytes' physical structural heterogeneity, creates extremely diverse habitats for other aquatic communities. Hence, fluvial and gravel pit lakes along the river-floodplains can be considered as hot spots of aquatic habitat diversity in the Western Balkans. However, these ecosystems are subjected to various human pressures such as alteration of hydrological regime, artificial land use of the riparian zone, sediment erosion, shoreline modification, and eutrophication in the entire region.