We studied the long‐term acclimatization of freshwater periphyton communities exposed to low and high ultraviolet radiation (UVR) intensities that simulate UVR doses received by lowland and high‐mountain streams of central Europe. To assess changes induced by UVR, we compared the community structure (species and biomass), function (photosynthetic yield), and tolerance to UVR and cadmium of periphyton growing in microcosms (artificial channels). On the basis of the rationale behind the pollution‐induced community tolerance concept, we expected that an increase in UVR tolerance would be through the replacement of more sensitive taxa by more tolerant taxa. After 38 d of exposure, periphyton in the high‐UVR treatment was dominated by Cyanobacteria, whereas diatoms dominated periphyton in the low‐UVR treatment. Concomitantly, the high‐UVR community increased its tolerance to UVR and showed cotolerance to cadmium (Cd). Structural changes contributing to this increased tolerance included an increase in UVR‐absorbing compounds, and the formation of cell aggregates that increased self shading. Induction of antioxidant enzymes after UVR and Cd exposure might be involved as defense mechanisms against oxidative stress. These changes reduced the exposure and effects of UVR, resulting in the protection of photosynthesis (high‐UVR photosynthetic yield was unaffected). A fivefold reduction in chlorophyll a in the high‐UVR treatment suggested that acclimatization had high metabolic costs. Additional experiments showed that even though biomass accrual offered some protection against UVR and Cd, the community changes experienced by the high‐UVR community contributed the most to UVR tolerance. Periphyton exposed to high UVR may experience simultaneous positive (tolerance to UVR and cotolerance to Cd) and negative effects (biomass reduction can increase accessibility by toxicants).