Temporary rivers are dynamic and complex ecosystems that are widespread in arid and semi-arid regions, such as the Mediterranean. Biotic communities adapted in their intermittent nature could withstand recurrent drought events. However, anthropogenic disturbances in the form of water stress and chemical pollution challenge biota with unpredictable outcomes, especially in view of climate change. In this study we assess the response of the biotic community of a temporary river to environmental stressors, focusing on water stress and pollution. Towards this aim, several metrics of four biotic groups (diatoms, macrophytes, macroinvertebrates and fish) were applied. All biotic groups responded to a pollution gradient mainly driven by land use, distinct functional groups of all biota responded to water stress (a response related to the rheophilic nature of the species and their resistance to shear stress), while the combined effects of water stress and pollution were apparent in fish. Biotic groups presented a differential temporal response to water stress, where diatom temporal assemblage patterns were explained by water stress variables of short-time response (15 days), while the responses of the other biota were associated to longer time periods. There were two time periods of fish response, a short (15 days) and a long-time response (60–75 days). When considering management decisions, our results indicate that, given the known response of river biota to pollution, biomonitoring of temporary rivers should also involve metrics that can be utilized as early warnings of water stress.