A study aimed at assessing the structure of rodent and shrew assemblages inhabiting a degradation gradient while considering rainfall patterns, was conducted in one of few remaining lowland tropical forests in Eastern Africa. We collected a unique dataset of rodents and shrews, representing 24 species (19 rodents, 5 shrews). The most abundant species alternated in dominance as species abundance significantly fluctuated across the study period following a degradation gradient (F2,33 = 5.68, p = 0.007). While only generalist species were observed near the degraded forest edge, habitat specialists such as Deomys ferrugineus, Malacomys longipes and Scutisorex congicus, were observed in the primary forest interior suggesting a significant (X2 = 1165.329, P<0.001) association between species and their associated habitats and habitat attributes. There was also an observed correlation between rainfall patterns and species abundance. Capturing more species in adjacent fallows and along the degraded forest edge suggests that many species are able to live in degraded habitats that offer a variety of food resources. The continued pressure on forest resources, however, may lead to changes in habitat structure. This, coupled with the dependence of forest ecological functions on rainfall, which is typically not the case, may ultimately cause the local extinction of highly specialized but less adaptable species.