Climate change is associated with altered environmental conditions and shifting mosaics of suitable habitats for organisms. Climate change in the form of drought can shift important lake shoreline habitats downslope, altering the lakes chemistry and habitat availability. Additionally, negative biological consequences can occur after a loss of submerged habitat along shorelines, hereafter littoral habitat. The objective of this study is to evaluate whether littoral habitat is lost (cobble, coarse woody habitat (fallen trees; CWH), and aquatic vegetation) under drought conditions across the United States. I used the National Lakes Assessment physical habitat data collected in summer 2012, when 75% of the U.S. experienced drought. I calculated the probability of cobble, CWH, and aquatic vegetation loss with lake level decline. I found cobble and CWH were highly vulnerable, where just 1 meter of lake level loss would result in nearly 100% habitat loss. Aquatic vegetation exhibited vulnerability but at a higher threshold. Multiyear drought will continue into the future with scientists estimating increases in drought frequency and severity, and we do not yet understand how or if aquatic animals will be resilient to a loss of littoral habitat. For example, previous research suggests food webs may be slow to recovery following littoral habitat loss. We must continue to evaluate the biological and environmental consequences of littoral habitat loss under drought conditions to successfully manage lakes and reservoirs into the future.