This paper reports the occurrence of the freshwater brown alga Heribaudiella fluviatilis (Areschoug) Svedelius in four new localities in southeastern Europe, as well as the first records for Croatia. Additionally, we report here a new type of substrate for H. fluviatilis, on stones in karstic rivers characterized by tufa formations. Despite a generally low number of findings, this and previous studies indicate that the species is not as rare as generally perceived; rather, it is overlooked, under-collected and therefore under-reported. The paper provides detailed diagnostic features of the thalli and habitats where the alga was found, with notes on corresponding vegetation, physical conditions and water chemistry. Additionally, along with the new records of the red alga Hildenbrandia rivularis (Liebmann) J. Agardh in Croatia, the associations of Heribaudiella-Hildenbrandia are reported for streams of Black Sea and Adriatic basins.