Hibernation requires balancing energy and water demands over several months with no food intake for many species. Many studies have considered the importance of fat for hibernation energy budgets because it is energy dense and can be stored in large quantities. However, protein catabolism in hibernation has received less attention and whole animal changes in lean mass have not previously been considered. We used quantitative magnetic resonance body composition analysis to measure fat and lean mass in two systems of hibernating bats, emphasizing the importance of lean mass for energy and water budgets. For cave myotis ( Myotis velifer ), lean mass represented 38 and 25% (male and female respectively) of pre-hibernation mass gain. In Townsend’s big-eared bats ( Corynorhinus townsendii ), lean mass accounted for 18 – 35% of mass change during hibernation, but lean only contributed 3 – 7% of the energy budget. Water is produced from the catabolism of both fat and lean, but net water production is much less than gross water production when accounting for the water required to excrete urea. Although most mammals can’t rely on protein catabolism for metabolic water production due to the water cost of excreting urea, we propose a variation on the protein-for-water strategy whereby hibernators could temporally compartmentalize the benefits of protein catabolism to periods of torpor, and the water cost to periodic arousals when free drinking water is typically available. Combined, our analyses demonstrate that lean mass is dynamic in hibernation, with important functional consequences for both energy and water budgets.