Inter-storm stable isotopic values of rainfall and throughfall for three flooding events were measured during the period of July to August 2011 to estimate their differences in a first-order chestnut watershed, Meilin, within the Taihu Lake basin. Comparison of δ(2)H and δ(18)O was conducted from four aspects: (1) sampling methods, (2) calculation methods, (3) stable isotopes and (4) flood events. Arithmetic and weighted incremental values of throughfall were generally lighter than those of rainfall. Isotopic composition of both incremental rainfall and throughfall exhibits marked temporal variation, particularly during large storm events; the former shows a higher variation than the latter. Differences of averaged precipitation and throughfall between storms were small, but individual storm variations were larger. Isotopic differences using different calculation methods are not significant; however, the differences resulting from sampling methods are of greater importance.