The range contraction and the decline in baiji abundance were caused by a combination of factors, including: possibly some level of direct exploitation historically; incidental mortality from interactions with fisheries; vessel traffic, management of navigation channels, and harbor construction; and loss or degradation of habitat by water development, land use practices, and pollution.

During China's "great leap forward" the baiji's traditionally venerated status as "goddess of the river" was denounced and baiji skin was used to produce handbags and gloves (Zhou and Zhang 1991).

Entanglement in fishing gear was estimated in the 1970s to 1980s to have been responsible for at least half of observed mortality (Lin et al. 1985, Zhou and Li 1989, Chen 1989, Chen et al. 1997). Longlines with thousands of unbaited hooks used for snagging bottom fish ("rolling hooks") accounted for 7 of 13 entanglement deaths recorded in the lower Yangtze between 1978 and 1985 (Zhou and Li 1989) and 15 of 28 in the middle reaches between 1973 and 1983 (Zhou and Wang 1994, also see Chen et al. 1997). Additional deaths from entanglement in rolling hooks were documented in the 1990s (Zhou et al. 1998). Baiji often have scars and open wounds from rolling hooks, and hook remains are sometimes found in the stomachs of dead animals (Lin et al. 1985, Zhou and Li 1989). Deaths also result from entanglement in gill and fyke nets (Zhou and Wang 1994). According to Zhou et al. (1998), both rolling hooks and fyke nets are banned in the Yangtze "because both are harmful to fisheries resources, and because of incidental killing of Baiji", but enforcement of these prohibitions is "very difficult" and therefore incidental mortality is likely to continue.

Electric fishing, although "strictly banned" in the Yangtze (Zhou et al. 1998), is widely practiced, particularly in the centre of the baiji's distribution (IWC 2001). By the early 2000s this fishing method had come to be viewed as the most important and immediate direct threat to the baiji's survival (Zhang et al. 2003). The electric shocks kill baiji outright (Chen and Hua 1989, Wang Ding in IWC 2001: 276) and unselectively kill other aquatic organisms, including the baiji's prey.

Propeller strikes have killed and injured baiji (Zhou and Zhang 1991, Chen et al. 1997) and are considered an increasing threat in view of the rapid industrial and economic growth of China, with its associated expansion of traffic on the Yangtze (Chen 1989, Chen and Hua 1989, Zhou and Li 1989, Zhou 1992, Zhou et al. 1998).

Explosives, used to deepen or widen river channels or for fishing, are another cause of baiji mortality (Lin et al. 1985, Zhou and Li 1989, IWC 2001).

Water development has transformed the baiji's habitat in important ways, e.g., by interrupting their movements upstream of dams, eliminating their access to tributaries and appended lakes, and reducing fish productivity (Liu et al. 2000). A dead baiji found at the bottom of a gate for a ship lock in a Yangtze tributary may have been killed accidentally by the structure (Liu et al. 2000). Chen and Hua (1987) predicted that the controversial Three Gorges Dam, completed in the early 2000s, would eliminate counter-current habitat for approximately 200 km downstream and degrade the existing counter-current systems for another 160 km downstream. Further, stratification in the reservoir will cause the water released below the dam to be cooler than previously, potentially affecting baiji and their prey. The downstream effects of Gezhouba Dam were not as extreme as those predicted for Three Gorges Dam because the former is a low-head, run-of-the-river structure (Zhong and Power 1996), meaning that sediment is allowed to pass through (which allows the formation of the counter-currents where baiji are generally found - see above) and no reservoir forms. Another effect of Three Gorges Dam will be to facilitate large ship traffic in the upper reaches of the Yangtze and thereby increase the amount of underwater noise and the incidence of vessel collisions with baiji (Chen and Hua 1989).

Industrial expansion and intensified agriculture (both facilitated by water development) have already caused major ecological problems in the Yangtze system. For example, Dongting and Poyang Lakes have become much shallower because of siltation from deforestation and agricultural development; in fact, it has been suggested that Dongting Lake could disappear altogether within a decade (Liu et al. 2000).

Pollutant loads in the Yangtze are expected to increase with industrialization and the spread of modern agricultural practices. Approximately 40% of China's industrial and agricultural output comes from the Yangtze basin, with more than 16 billion cubic meters of wastewater discharged into the river annually, of which more than 12 billion cubic meters is industrially polluted and largely untreated (Zhou et al. 1998).