Current patterns of worldwide population declines and species extinction have been attributed to the destruction, fragmentation, and degradation of natural areas. Much research has thus far focused on estimating how populations respond to changes in the amount and configuration of available habitat. I addressed this question by testing for effects of habitat fragmentation on forest bird species in southwestern Costa Rica. I tested for fragmentation effects on survival of adult individuals of the whiteruffed manakin (Corapipo altera), and found a significant difference in annual apparent survival rates for adults marked and recaptured in forest fragments vs. a larger forest reserve. Therefore, habitat loss and fragmentation is likely driving the dynamics of manakins by lowered population growth rates through reductions in survival. I used the same manakin population to test for population structuring and genetic diversity. Individuals from all fragments comprised a single genetic population, and that the fragments were likely at migration-drift equilibrium. I found only modest levels of differentiation, and did not detect a correlation between genetic diversity and fragment size. If community-level effects using a dynamic, multi-species hierarchical model applied to observational data. I found higher levels of occupancy and colonization of forest across species in contrast to the non-forest matrix. Species' prior classification of forest dependency was a poor predictor of overall occupancy dynamics of both habitat types. I lastly tested for effects on habitat quality, and found an effect of reduced area on composition and abundance of forest interior tree species relative to pioneer species. There was also an effect on tree height in forest fragments relative to control sites, dependent on the canopy strata of the tree (t= 5.20, p less than 0.0001). Therefore, deforestation could potentially reduce the quality of forest fragments for tropical bird communities through changes in food resources and availability of microhabitats, as observed by changes in the structure and composition of the tree community. Estimating how tropical bird populations respond to deforestation, through effects on survival, dispersal, and occupancy dynamics, has furthered our understanding on how organisms in diverse communities respond to anthropogenic changes in the environment.