Correctly estimating nitrogen loss in the sediments is of great significance for our understanding of the nitrogen cycle in the freshwater ecosystems. The revised 15N isotope pairing techniques (rIPT) can simultaneously estimate the denitrification and anammox rates and their contributions to the nitrogen loss in intact core sediments. In the present study, we compared the applicability of the rIPTra whose parameter was related to the slurry incubations, and the rIPTV whose parameter was derived directly from the intact core incubations, and estimated nitrogen loss rates of different sedimentary environments in Lake Taihu in autumn using the continuousflow intact core incubation instrument. The main results were as follows. (1) The occurrence of denitrification and anammox in Meiliang Bay and Xuhu Bay was proved using the slurry incubations. (2) The basic assumptions of the rIPT were hold. And the rIPTV was of higher accuracy because of the independency between the in situ nitrogen loss rates estimated using the rIPT and the addition of 15NO-3 in both Meiliang and Xuhu Bays. (3) Based on the rIPTV, the denitrification, anammox, and nitrogen loss rates were estimated as 3.09, 1.47, and 4.56 μmol/(m2·h) in Meiliang Bay, while those rates were 0.69, 0.02, and 0.71 μmol/(m2·h) in Xuhu Bay. (4) Compared with the rIPTV, the rIPTra provided a nitrogen loss rate approximating to that from rIPTV in sediments where the ra was low (3.3%), while the rIPTra would overestimate the nitrogen loss rates and underestimate the anammox contribution in sediments where the ra was high (32.2%).