Mechanical and fire treatments are commonly used to reduce fuels where land use practices have encouraged accumulation of woody debris and high densities of trees. Treatments focus on restoration of vegetation structure, but will also affect wildlife populations. Small mammal populations were monitored before and after dense tree stands were thinned on 2,800 ha in NM, U.S.A. Mammals were live-trapped in upland and riparian habitats from 2002 to 2006 in thinned and unthinned forests. Populations of deer mice (Peromyscus maniculatus) and voles (Microtus spp.) were estimated using mark–recapture data. An index of abundance was used for chipmunks (Tamias spp.) and woodrats (Neotoma spp.). Deer mice responded positively to thinning in 2005 in upland and riparian habitats. Voles responded positively to thinning in 2005 and 2006 in riparian habitats. There was no change related to thinning in relative abundance of chipmunks and woodrats or in total small mammal biomass. Because abiotic processes affect wildlife populations, we also examined response of deer mouse populations to precipitation. After removing treatment effects, populations were modeled with winter and summer precipitation. In both upland and riparian habitats, deer mouse populations had a curvilinear response to precipitation from the preceding winter, while responding negatively to summer rainfall only in riparian habitats. Increases in deer mice populations occurred on thinned sites during a year of high winter precipitation, generally associated with depressed populations, indicating that forest thinning moderated this relationship. Results suggest that precipitation plays a role in determining timing and presence of response to restoration treatments.