Underwater sound plays an important role in some critical life functions of many aquatic animals. Underwater noise pollution has received relatively more attention in ocean systems. However, little attention has been paid to freshwater systems, such as the Yangtze River which is the habitat of critically endangered Yangtze finless porpoises (Neophocaena asiaeorientalis asiaeorientalis). In 2012, the underwater noise levels in 25 sites along the middle and lower sections of the Yangtze River were measured. The root mean square sound pressure level (SPL) and unweighted sound exposure level (SEL) at each site ranged between 105 ± 2.4 (median ± quartile deviation) and 150 ± 5.5 dB. Obvious spatial and temporal variations in the SPL were detected among the 25 sites. The SPL and SEL in the middle section of the Yangtze River were smaller (approximately 15 dB) and fluctuated more compared to those in the lower section. The power spectrum in the mainstem was site specific. However, all the spectra levels were higher than the audiogram of Yangtze finless porpoises. Majority of the sites had an averaged cumulative unweighted SEL (72%) and cumulative weighted SEL (68%) that surpassed the underwater acoustic thresholds for onset of hearing temporal threshold shifts for finless porpoise. Porpoise bio-sonars were detected in 89% of sonar monitoring sites indicating that noise pollution in the Yangtze River greatly threatened porpoise survival. In 8% of the sites, the averaged cumulative weighted SEL exceeded that of underwater acoustic thresholds causing non-recoverable permanent threshold shifts of finless porpoises auditory system whereas it was less than 1 dB below the underwater acoustic thresholds in other 8% of the sites. These sites urgently needed noise mitigation and management strategies. These results will facilitate the evaluation of the impacts of anthropogenic noise pollution on local finless porpoises and give further guidelines on its effective conservation.