Climate projection studies of future changes in snow conditions and resulting rain-on-snow (ROS) flood events are subject to large uncertainties. Typically, emission scenario uncertainties and climate model uncertainties are included. This is the first study on this topic to also include quantification of natural climate variability, which is the dominant uncertainty for precipitation at local scales with large implications for runoff projections, for example. To quantify natural climate variability, a weather generator was applied to simulate inherently consistent climate variables for multiple realizations of current and future climates at 100 m spatial and hourly temporal resolution over a 12×12 km high-altitude study area in the Swiss Alps. The output of the weather generator was used as input for subsequent simulations with an energy balance snow model. The climate change signal for snow water resources stands out as early as mid-century from the noise originating from the three sources of uncertainty investigated, namely uncertainty in emission scenarios, uncertainty in climate models, and natural climate variability. For ROS events, a climate change signal toward more frequent and intense events was found for an RCP 8.5 scenario at high elevations at the end of the century, consistently with other studies. However, for ROS events with a substantial contribution of snowmelt to runoff (> 20 %), the climate change signal was largely masked by sources of uncertainty. Only those ROS events where snowmelt does not play an important role during the event will occur considerably more frequently in the future, while ROS events with substantial snowmelt contribution will mainly occur earlier in the year but not more frequently. There are two reasons for this: first, although it will rain more frequently in midwinter, the snowpack will typically still be too cold and dry and thus cannot contribute significantly to runoff; second, the very rapid decline in snowpack toward early summer, when conditions typically prevail for substantial contributions from snowmelt, will result in a large decrease in ROS events at that time of the year. Finally, natural climate variability is the primary source of uncertainty in projections of ROS metrics until the end of the century, contributing more than 70 % of the total uncertainty. These results imply that both the inclusion of natural climate variability and the use of a snow model, which includes a physically based process representation of water retention, are important for ROS projections at the local scale.