In the context of climate change, with an increase in the incidence of seasonally dry streambeds, we examined the impact of drought, and its duration, on the structure of diatom communities and the consequences of this on diatom index values (Biological Diatom Index; Specific Polluosensitivity Index) in the Mediterranean river Maureillas. The effects of several durations of droughts or low flow events (1, 2 and 4 weeks) on diatom‐dominated biofilms were studied by removing pebbles from the river and comparing the growing communities after rewetting with those of control biofilms (pebbles left in the streambed) and with those of newly formed biofilms (cleaned‐up pebbles). Sampling was performed six times during the 28‐day rewetting phase. We determined the specific composition of diatom communities, the mortality rate after rewetting, and the Biological Diatom Index and Specific Polluosensitivity Index scores for each sample, distinguishing between potentially living diatoms (full frustules with chloroplasts) and dead diatoms (empty frustules). Our results showed a notable and durable impact of even short drought on diatom communities. The different trajectories of biofilm communities observed between the types of pebbles showed the importance of the biofilm history for the community structure. This should be taken into account to improve the sampling practices used for monitoring. We also observed a stable mortality rate whatever the drought duration was. Diatom index values were stable despite the observed impact of treatment on diatom communities. These results emphasize the reliability of the diatom index to evaluate biological quality according to European requirements. In addition, the distinction of empty and full frustules did not induce significant differences, but it may reduce biases in interpretation. Copyright © 2014 John Wiley & Sons, Ltd.