Vegetation management on levees, especially removal of trees and shrubs, might affect burrowing mammals that are considered threats to levee integrity. We evaluated habitat associations of California ground squirrels (Otospermophilus beecheyi) and Botta's pocket gophers (Thomomys bottae) on levees in the Sacramento Valley to assess the effects of levee vegetation management on these species. Using burrows as an indirect measure of mammal presence, we found that the presence of trees had a negative effect on the occurrence and abundance of ground squirrels on levees, and on the location of their burrowing activities on the levee slope, potentially because visual occlusion caused by tall woody vegetation impedes detection of predators. Similarly, trees had a negative effect on the abundance of pocket gophers on levees and on the location of their burrowing activities on the levee slope, probably because of the effect of tree cover on food availability. The conversion of woodland habitats to grasslands on levees most likely will result in increased occurrence, abundance, or both of ground squirrels and pocket gophers, and thereby increase the potential threat that their burrowing activities pose to levee integrity. © 2012 The Wildlife Society.