Biological soil crusts across the desert regions play a key role in regional ecological security and ecological health. They are vital biotic components of desert ecosystems that maintain soil stability, fix carbon and nitrogen, influence the establishment of vascular plants, and serve as habitats for a large number of arthropods and microorganisms, as well as influencing soil hydrological processes. Changes in temperature and precipitation are expected to influence the functioning of desert ecosystems by altering biotic components such as the species composition of biological soil crusts. However, it remains unclear how these important components will respond to the prolonged warming and reduced precipitation that is predicted to occur with climate change. To evaluate how the hydrological properties of these biological soil crusts respond to these alterations, we used open‐top chambers over a 10‐year period to simulate warming and reduced precipitation. Infiltration, dew entrapment, and evaporation were measured as surrogates of the hydrological functioning of biological soil crusts. It was found that the ongoing warming coupled with reduced precipitation will more strongly affect moss in crustal communities than lichens and cyanobacteria, which will lead to a direct alteration of the hydrological performance of biological soil crusts. Reductions in moss abundance, surface cover, and biomass resulted in a change in structure and function of crustal communities, decreased dew entrapment, and increased infiltration and evaporation of biological soil crusts in desert ecosystems, which further impacted on the desert soil water balance. Warming coupled with reduced precipitation will more strongly affect moss in crustal communities than lichens and cyanobacteria. Reductions in moss abundance, surface cover, and biomass resulted in a change in structure and function of crustal communities, which will lead to a direct alteration of the hydrological performance of biological soil crusts.