Simple SummaryRelocation of endangered freshwater cetaceans in natural reserves is an effective conservation strategy to recover their populations. However, due to historical reasons, some natural reserves have facilities that cannot be removed, such as water intake pontoons that are important for residents nearby. These facilities generate underwater noise which may affect cetaceans. To investigate the potential impacts of underwater noise from water intake pontoons on freshwater cetaceans, this study measured such noise within a Yangtze finless porpoise (Neophocaena asiaeorientalis) nature reserve, analyzed its effects on porpoise behavior, vocalization, and hearing, and explored porpoise adaptation to the transient holding pen environment. This study provides a reference for assessing whether human facilities have impacts on freshwater cetaceans.Underwater noise pollution caused by human activities may affect freshwater cetaceans to different degrees. To analyze the impacts of water intake pontoons on Yangtze finless porpoises (Neophocaena asiaeorientalis), this study collected underwater noise data from such a pontoon in a nature reserve, plotted the power spectral density of acoustic signals, and calculated the root mean square sound pressure levels and the magnitude of sound source levels. The 1/3-octave sound pressure level root mean square values at the transient holding pens were <18.0 kHz, 39.5−60.0 kHz, which were slightly higher than the Yangtze finless porpoise hearing threshold curve values and therefore could be perceived. However, the results indicated that the porpoises would not develop a temporary hearing threshold shift. Meanwhile, pontoon noise did not interfere with the porpoises’ high-frequency acoustic signal nor did it affect their echolocation; it significantly interfered with their low-frequency acoustic signal, however, and the mother–child communication of the finless porpoises was affected, but this effect was quickly compensated due to the limited space range of the holding pens. Through this study of Yangtze finless porpoises, this paper provides a reference for assessing whether human facilities have impacts on freshwater cetaceans.