Climate change is affecting the phenology of organisms and ecosystem processes across a wide range of environments. However, the links between organismal and ecosystem process change in complex communities remain uncertain. In snow-dominated watersheds, snowmelt in the spring and early summer, followed by a long low-flow period, characterizes the natural flow regime of streams and rivers. Here, we examined how earlier snowmelt will alter the phenology of mountain stream organisms and ecosystem processes via an outdoor mesocosm experiment in stream channels in the Eastern Sierra Nevada, California. The low-flow treatment, simulating a 3- to 6-wk earlier return to summer baseflow conditions projected under climate change scenarios in the region, increased water temperature and reduced biofilm production to respiration ratios by 32%. Additionally, most of the invertebrate species explaining community change (56% and 67% of the benthic and emergent taxa, respectively), changed in phenology as a consequence of the low-flow treatment. Further, emergent flux pulses of the dominant insect group (Chironomidae) almost doubled in magnitude, benefitting a generalist riparian predator. Changes in both invertebrate community structure (composition) and functioning (production) were mostly fine-scale, and response diversity at the community level stabilized seasonally aggregated responses. Our study illustrates how climate change in vulnerable mountain streams at the rain-to-snow transition is poised to alter the dynamics of stream food webs via fine-scale changes in phenology-leading to novel predator-prey matches or mismatches even when community structure and ecosystem processes appear stable at the annual scale.