Knowledge of the isotopic composition in precipitation is of importance for studies using isotopic composition as hydrological tracers to investigate recharge sources of groundwater, hydrograph separation, and paleoclimate reconstruction. In catchments with vegetation cover, major water isotope inputs are throughfall instead of precipitation. Thus, it is necessary to know how much precipitation isotopic composition is altered by vegetation canopy, and how this alteration varies with different vegetation covers. However, few studies have examined these issues with continuous monitoring and for typical vegetation covers in South Australia. In this study, we investigate the stable isotopic composition of throughfall over two vegetation surfaces (pine plantation and native eucalyptus forest), with bulk precipitation and throughfall samples collected from September, 2009 to October, 2010 with an average 18-day interval, together with intra-event precipitation samples collected at a nearby location, from September, 2009 to February, 2013. We synthesized a conceptual framework for throughfall isotopic composition including the effects of intra-event selection and inter-event selection, and partial evaporation using δ18O and d-excess. The results indicate that the selection processes, either within individual events, or between events, or both, contribute to throughfall isotopic composition over the two vegetation covers, with less important but observed effects from partial evaporation. Pine plantation site with a denser vegetation cover has experienced larger alteration in throughfall isotopic composition. The significance of the difference between throughfall and precipitation isotopic compositions for groundwater sources, hydrograph separation and paleoclimate reconstruction studies are also discussed.