This study explored biotic and abiotic causes for spatio-temporal variation in soil respiration from surface litter, roots, and soil organic matter over one year at four rain forest sites with different vegetation structures and soil types in the eastern Amazon, Brazil. Estimated mean annual soil respiration varied between 13–17 t C ha−1 yr−1, which was partitioned into 0–2 t C ha−1 yr−1 from litter, 6–9 t C ha−1 yr−1 from roots, and 5–6 t C ha−1 yr−1 from soil organic matter. Litter contribution showed no clear seasonal change, though experimental precipitation exclusion over a one-hectare area was associated with a ten-fold reduction in litter respiration relative to unmodified sites. The estimated mean contribution of soil organic matter respiration fell from 49% during the wet season to 32% in the dry season, while root respiration contribution increased from 42% in the wet season to 61% during the dry season. Spatial variation in respiration from soil, litter, roots, and soil organic matter was not explained by volumetric soil moisture or temperature. Instead, spatial heterogeneity in litter and root mass accounted for 44% of observed spatial variation in soil respiration (p < 0.001). In particular, variation in litter respiration per unit mass and root mass accounted for much of the observed variation in respiration from litter and roots, respectively, and hence total soil respiration. This information about patterns of, and underlying controls on, respiration from different soil components should assist attempts to accurately model soil carbon dioxide fluxes over space and time.