We studied the relationships between environmental variables and the physiology of two (semi-)aquatic mosses (Bryum pseudotriquetrum and Fontinalis antipyretica) in an unforested headwater stream over a three year period. Neither environmental or physiological variables showed significant interannual variations. Most environmental variables (water temperature, stratospheric ozone, and photosynthetic, UV-A and UV-B radiation) showed distinct seasonal variations, but only a few physiological ones did. In both species, photoprotection variables (the activity of the xanthophyll cycle and the bulk UV absorbance of the methanol-extractable UV-absorbing compounds, MEUVAC) varied more seasonally than variables related to physiological activity, such as the sclerophylly index and chlorophyll fluorescence parameters (F_v/F_m and Φ_PSII). Changes in physiological activity would be attenuated by the buffering capacity of water with respect to the influence of environmental factors, and dynamic variables like F_v/F_m and Φ_PSII would be little determined by cyclic environmental factors. In B. pseudotriquetrum, both MEUVAC and kaempferol 3,7-O-diglycoside (a potentially UV-protective flavonoid) were positively associated with radiation levels, whereas in F. antipyretica photoprotection mechanisms were not correlated with any environmental variable. In addition, MEUVAC was 3–4 fold higher in B. pseudotriquetrum than in F. antipyretica. Thus, different photoprotection mechanisms, with a different environmental regulation, can be suggested for these two species. DNA damage was not found in any sample, probably because both species displayed efficient DNA repair mechanisms.