To assess the influence of vegetation structure on the isotopic composition of rainwater input during its passage through the canopy, rainfall, throughfall, stemflow and soil water were collected at a tropical seasonal rain forest (TSRF) stand and a rubber plantation (RP) stand for stable isotopic analysis during the 3 year period 2002–2004. The result clearly shows that the rainfall partitioning and the isotopic composition of throughfall, stemflow and soil water were strongly influenced by the forest canopy structure. Although the differences of overall mean isotopic composition of throughfall and stemflow between the two forests were small and not significantly different (P>0.05), greater differences were found when only light rain events (≤10 mm) were taken into consideration. During the dry season, the enriched isotopic composition and the smaller slope of the regression line of δ18O versus δD for soil water in the TSRF is not an indication that it lost significant water by evaporation, but a mixture of enriched fog drip, throughfall and stemflow. However, the soil in the RP stand showed significant evaporation. During the rainy season, the soil water for both stands did not appear to display considerable evaporation effects.