Karst freshwater habitats are globally recognized biodiversity hotspots that harbor numerous endemic and threatened species within their unique ecological frameworks. Despite this, karst freshwater ecosystems remain poorly understood with respect to the distribution and ecology of algae. This study aims to fill existing knowledge gaps by investigating karst springs across the Dinaric and Carpathian–Balkan Mountains in Serbia. Field research was conducted from April 2017 to November 2025, during which samples of macroscopic algal aggregations were collected from 17 karst springs, and physical and chemical water parameters were measured. Based on morphological characteristics, 11 distinct types of macroscopic aggregations were recognized: tufts (Audounella sp.), free filaments (Paralemanea torulosa, Tribonema viride, Microspora amoena), mucilaginous filaments (Batrachospermum sensu lato), mucilaginous colonies (Chaetophoropsis elegans), cushion-like forms (Vaucheria spp.), encrusting mats (Riverina rivularis, Gongrosira spp.), cyanobacterial mats (Microcoleus autumnalis, M. vaginatus, Phormidium nigrum), brown threads (Melosira varians, Odontidium hyemale and O. mesodon), green threads (Spirogyra sp., O. mesodon and Diatoma moniliformis; Microspora pachyderma and O. hyemale), brown gelatinous threads (O. hyemale, O. mesodon, M. varians, and chironomid eggs) and green gelatinous threads (Tribonema affinis, O. mesodon, M. varians, and chironomid eggs). Among the recorded macroalgae, the red alga Batrachospermum sensu lato was the most frequently observed, occurring in 15 karst springs, followed by R. rivularis, recorded in six localities. In contrast, the occurrence of P. torulosa, C. elegans, Ph. nigrum, M. autumnalis, and M. vaginatus was highly restricted, with each taxon being recorded in only one of the surveyed karst springs. Our study emphasizes the importance of Serbian karst springs as habitats for rare freshwater red algae, such as Batrachospermum sensu lato, R. rivularis, and P. torulosa. Protecting these springs is crucial, as any changes in water quality or flow could threaten these sensitive species.