The Yangtze finless porpoise (Neophocaena asiaeorientalis asiaeorientalis) is an endangered freshwater porpoise subspecies unique to the Yangtze River basin. Seasonal variations in local distribution of the animal, as well as fish presence, sand dredging, ship navigation, and bridges were examined as potential factors affecting the occurrence of the animals. Passive acoustic surveys were performed regularly from May 2007 to August 2010, near the conjunction of the Yangtze River and Poyang Lake. The distribution of the porpoises was seasonally site-specific. In May and August, the animals were detected more often at river junctions than in the lake, but vice versa from November to February. The rate of the porpoise detection was significantly higher in areas of fish presence than in areas of absence. The number of porpoises detected did not differ significantly between the sand dredging operation and the prohibition period (in 2008), although the number of vessels obviously declined in 2008. Ship traffic and bridges also did not appear to affect the presence of porpoises. These results showed the relative importance of the various environmental factors, which is important for conservation of not only Yangtze finless porpoise but also endangered isolated cetaceans.