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Mediterranean rivers are subjected to strong seasonality with drought during the hot season and extreme flows in autumn-winter. In particular, drought episodes and water scarcity alter the river morphology, with repercussions on primary production and the trophic chain. In this paper, we aimed at analysing the different responses in terms of chlorophyll a content of the three main photosynthetic groups composing stream periphyton, namely diatoms, cyanobacteria and green algae. This work was conducted in the Ligurian Alps (NW-Italy) on five oligotrophic streams (Argentina, Impero, Merula, Quiliano and Vallecrosia), similar in terms of physico-chemical parameters. We measured chlorophyll a content of diatoms, cyanobacteria and green algae by means of an in situ fluorimetric probe (BenthoTorch®). Data were collected from April to October 2014 in: i) impacted sites, where the water scarcity was exacerbated by human pressure; ii) control sites. We applied Generalized Linear Mixed Models to investigate the response of total chlorophyll a and its relative proportions among the three algal groups in relation to the following environmental predictors: water depth, flow velocity, canopy shading, microhabitat isolation, sampling season, dissolved oxygen, temperature, pH, nutrients, and macrophyte coverage.Results showed an opposite response of diatoms and green algae. Diatoms were favoured in the control sites and under moderate flow conditions, while the probability of green algae presence was higher in the impacted sites and during the drought season. Cyanobacteria showed a response similar to green algae, preferring warm, isolated pools typical of the drought period. Diatoms proved to be the most sensitive to drought. More specifically, we found out that percentages of diatoms below 51% with respect to total benthic chlorophyll a indicate high hydrological disturbance. This study provides the first evidence that the proportion of chlorophyll a produced by diatoms can be a suitable indicator for monitoring programs aiming at determining the effects of water scarcity on river ecosystems.