<p>Rain events in arid environments are highly unpredictable, interspersing extended periods of drought. Therefore, tracking changes in desert soil bacterial communities during hydration-desiccation cycles in the field, was seldom attempted. Here, we assessed rain-mediated dynamics of active community in the Negev Desert biological soil crust (biocrust), and evaluated the changes in bacterial composition, potential function, photosynthetic activity, and extracellular polysaccharide (EPS) production. We predicted that increased biocrust moisture would resuscitate the phototrophs, while desiccation would inhibit their activity. Our results show that hydration increased chlorophyll content, resuscitated the biocrust <em>Cyanobacteria</em>, enhanced EPS production, and induced potential phototrophic functions. However, decrease in the soil water content did not immediately decrease the phototrophs activity, though chlorophyll levels decreased. Moreover, while the <em>Cyanobacteria</em> relative abundance significantly increased, <em>Actinobacteria</em>, the former dominant taxa, significantly decreased in abundance. We propose that, following a rain event, the response of the active bacterial community lagged the soil moisture content due to the production of EPS which delayed the desiccation of the biocrust community.</p>