In 2009 the Water Framework Directive added aquatic plants to European river quality checks. In Bulgaria, aquatic mosses became key indicators. Two species of the Fontinalis genus, *Fontinalis antipyretica* and *Fontinalis hypnoides*, were studied to clarify their role. Scientists collected 421 field samples between 2009 and 2024, plus data from literature and herbariums. Only field data were used for analysis. *F. antipyretica* appeared in about 11 % of sites, while *F. hypnoides* was found in just 1 %. This shows the former is more tolerant: it lives at various elevations, in variable currents, and in water with conductivity from 31 to 4 380 µS cm⁻¹ and total nitrogen from 0.07 to 3.3 mg L⁻¹. The latter prefers cleaner water, with stable pH and nitrogen below 1 mg L⁻¹. Their co‑occurrence in some stretches suggests they share some plant companions, but have different chemical needs. These differences help refine the Reference Index, a score that tells how close a river is to natural conditions. In the future, *F. hypnoides* could become a sharper signal of pristine water, while *F. antipyretica* will indicate more resilient environments.
The Reference Index (RI) is a WFD tool that combines the presence of sensitive and tolerant species to assess a watercourse's ecological status. Fontinalis species are classified into ecological groups: *F. antipyretica* belongs to group B (indifferent), while *F. hypnoides* belongs to group A (reference indicator). This distinction is based on bio‑physical parameters measured in 421 field samples, complemented by 73 literature records and 43 herbarium specimens. A multivariate logistic regression model was used for statistical analysis, revealing a strong correlation between *F. hypnoides* presence and pH values between 7.0 and 8.0 and total nitrogen below 1 mg L⁻¹. In contrast, *F. antipyretica* shows a flatter response, tolerating conductivity up to 4 380 µS cm⁻¹ and nitrogen up to 3.3 mg L⁻¹. Elevation variability (50–1 200 m a.s.l.) suggests a broader thermal adaptation for *F. antipyretica*. Co‑occurrence analysis showed both species share macrophyte assemblages such as *Potamogeton* spp. and *Ceratophyllum demersum*, but *F. hypnoides* is more frequently linked to high‑quality biological communities, characterized by low phosphate concentrations and a higher presence of filamentous algae. These findings support the use of *F. hypnoides* as a bio‑indicator of reference conditions, enhancing the RI's ability to distinguish slightly degraded from near‑natural rivers. Moreover, the broader ecological amplitude of *F. antipyretica* makes it useful for detecting environmental stress gradients along a watercourse, providing complementary information for integrated water resource management. Integrating these data into the national database will allow periodic RI updates, improving the precision of ecological assessments required by the Water Framework Directive.
