A comprehensive survey of Croatian watercourses covering the whole of the national territory and investigating inherent watercourse heterogeneity was conducted to explore the ecological responses of the most frequent freshwater bryophytes with respect to water chemistry variables and land use within the catchment area. Direct multivariate ordination (CCA) of vegetation data paired with 18 environmental variables revealed that freshwater bryophytes and their assemblages were segregated along the gradients of water chemistry and the proportion of natural and urban area within the catchment. Generalized additive models (GAM) were employed to explore the ecological responses of individual species. The results showed that most of the investigated species preferred natural, clean, well-oxygenated watercourses, with low nutrient and organic matter content, as well as with low electrical conductivity. Species such as Palustriella falcata, Eucladium vertcillatum, Dichodontium flavescens and Jungermannia atrovirens had narrow ecological niches and were restricted to pristine watercourses, while the most frequent and widely distributed species, such as Fontinalis antipyretica, Rhynchostegium riparioides, Cratoneuron filicinum, Fissidens crassipes, Cinclidotus fontinaloides and C. riparius, had a wide ecological tolerance. Riccia fluitans and Leptodyctium riparium had wide ecological ranges, but with optima in hypereutrophic waters with high nutrient and organic content, as well as high electrical conductivity. Furthermore, these two species were frequently associated with a high share of intensive agriculture and a low share of natural land within the catchment.