While previous studies have focused on impacts of average climate change on Russian agriculture and water resources, this study takes into account the impact of changing frequency and spatial heterogeneity of extreme climate events, and the reliance of most of Russia on a few food producing regions. We analyze impacts of the IPCC A2 and B2 climate scenarios with the use of the Global Assessment of Security (GLASS) model (containing the Global Agro-Ecological Zones (GAEZ) crop production model and the Water-Global Assessment and Prognosis (WaterGAP 2) water resources model). As in previous studies we find that decreased crop production in some Russian regions can be compensated by increased production in others resulting in relatively small average changes. However, a different perspective on future risk to agriculture is gained by taking into account a change in frequency of extreme climate events. Under climate normal conditions it is estimated that “food production shortfalls” (a year in which potential production of the most important crops in a region is below 50% of its average climate normal production, taking into account production in food-exporting regions) occur roughly 1–3 years in each decade. This frequency will double in many of the main crop growing areas in the 2020s, and triple in the 2070s. The effects of these shortfalls are likely to propagate throughout Russia because of the higher likelihood of shortfalls occurring in many crop export regions in the same year, and because of the dependence of most Russian regions on food imports from a relatively few main crop growing regions. We estimate that approximately 50 million people currently live in regions that experience one or more shortfalls each decade. This number may grow to 82–139 million in the 2070s. The assessment of climate impacts on water resources indicates an increase in average water availability in Russia, but also a significantly increased frequency of high runoff events in much of central Russia, and more frequent low runoff events in the already dry crop growing regions in the South. These results suggest that the increasing frequency of extreme climate events will pose an increasing threat to the security of Russia's food system and water resources.