We measured soil oxygen concentrations at 10 and 35 cm depths and indices of biogeochemical cycling in upland forest soils along a rainfall and elevation gradient (3500– 5000 mm y−1; 350–1050 masl) and along topographic gradients (ridge to valley, 150 m) in the Luquillo Experimental Forest, Puerto Rico. Along the rainfall gradient, soil O2 availability decreased significantly with increasing annual rainfall, and reached very low levels (<3%) in individual chambers for up to 25 consecutive weeks over 82 weeks of study. Along localized topographic gradients, soil O2 concentrations were variable and decreased significantly from ridges to valleys. In the valleys, up to 35% of the observations at 10–35 cm depth were <3% soil O2. Cross correlation analyses showed that soil O2 concentrations were significantly positively correlated along the topographic gradient, and were sensitive to rainfall and hydrologic output. Soil O2 concentrations in valley soils were correlated with rainfall from the previous day, while ridge sites were correlated with cumulative rainfall inputs over 4 weeks. Soils at the wettest point along the rainfall gradient had very high soil methane concentrations (3–24%) indicating a strong influence of anaerobic processes.We measured net methane emission to the atmosphere at the wettest sites of the rainfall gradient, and in the valleys along topographic gradients. Other measures of biogeochemical function such as soil organic matter content and P availability were sensitive to chronic O2 depletion along the rainfall gradient, but less sensitive to the variable soil O2 environment exhibited at lower elevations along topographic gradients.