Interactions among multiple stressors generated by global change exert cumulative effects on ecosystems. In order to identify the long-term interactive effects of ultraviolet radiation (UVR) and increasing atmospheric nutrient inputs (P-inputs) on aggregate (growth rate, chlorophyll a and abundance) and emergent (evenness and diversity) algal community variables, a 2 × 5 factorial experiment [two levels of light quality (+UVR, −UVR) and five levels of nutrient enrichment] was conducted using in situ mesocosms in a high-mountain lake in the Sierra Nevada (Spain) over a 70-day period. Addition of P suppressed and inverted the stimulatory UVR effect on the non-flagellate growth rate (mid-term scale). This interactive effect was propagated as increased harmful UVR effect on chlorophyll a and abundance across the P-gradient. Interestingly, P-pulse reversed the positive effect of UVR on phytoplankton evenness and diversity on the long-term scale. These findings support our hypothesis that the UVR × P interactive effect would favor a few UVR-tolerant rapid-growing species. We show that the algal community is acclimated to UVR-flux but not to high P-pulse. The loss of diversity and disappearance of mixotrophic flagellates may have important implications for the functioning of clear-water ecosystems.