Threats include incidental mortality in fishing gear, deliberate killing for fish bait and attractant and for predator control, damming of rivers (although this is, at present, less of a problem than for the river cetaceans in Asia), and environmental pollution from organochlorines and heavy metals (see da Silva 2002; IWC 2007; Reeves et. Al. 1999).

The Mura Indians hunted botos near Barro do Rio Negro, Brazil during the nineteenth century (Pilleri and Arvy 1981) and the Tucuna and Cocama Indians may have killed them in the Amazon near Leticia (Allen and Neil 1958; Layne and Caldwell 1964) and the lower Ucayali River (Mohr 1964), respectively, until at least the 1950s.

Between 1956 and the early 1970s, more than 100 botos were live-captured and exported mostly to the U.S. and Europe (Brownell 1984) and (a few) to Japan (Tobayama and Kamiya 1989). However, in recent decades, there have been no reported live-captures and exports.

Incidental mortality has not been studied systematically in most areas. However, similar to other small cetaceans, botos are vulnerable to entanglement in a variety of nets (lampara seine nets, fixed gill nets, drifting gill nets; Best and da Silva 1993; Martin et al. 2004) as well as to drop traps intended to catch large fish or manatees in the flooded forest in Peru (Leatherwood 1996)

There is an emergent, but already large-scale, problem involving the deliberate killing of botos in Brazil for fish attractant (IWC 2007). Botos are also killed deliberately in some areas because fishermen regard them as competitors and because the dolphins damage fishing nets (F. Trujillo pers. comm. to B.D. Smith).

Fishing with explosives, although illegal in most areas, is common in some areas of the Amazon Basin (Goulding 1983; Smith 1985). This fishing technique threatens botos due to the concussive effects of explosions. Fishermen also reportedly attempt to kill dolphins that are attracted to prey on the stunned or dead fish (Best and da Silva 1989a).

Water development projects have not been as extensive in the Amazon and Orinoco basins as in Asian rivers inhabited by cetaceans. A population of botos was isolated above the Tucuruí dam in the Tocantins River, but there is no information on their current status. The Balbina dam in the Uatuma River may have isolated botos but there is no information on historic or current occurrence of dolphins in this river. Both of these dams in the Amazon basin, and the Guri dam in the Caroní, an Orinoco tributary, have probably degraded downstream habitat due to their effects on flow and temperature regimes (see Ward and Stanford 1989; Ligon et al. 1995; Kondolf 1997). There are many more proposed dams, especially for northward flowing Amazon tributaries that, if built, would restrict dolphin movements (Best and da Silva 1989a) and probably degrade their habitat.

Mercury is often used to separate gold from soil and rock in mining operations along the Amazon (Pfeiffer ,i>et al. 1993). In the Madeira River almost 60% of children under five years old had accumulated levels of mercury, presumably from eating contaminated fish, high enough to cause neurological damage (Boischio and Henshel 1996). A study of mercury in the sediments and floating plants in the Tucuruí Reservoir of the former Tocantins River, Brazil, emphasized the risk of mercury accumulation in the bed of non-flowing waters (Aula et al. 1995). The effects of the bioaccumulation of mercury in botos are unknown but the high levels recorded in the Amazon ecosystem give reason for concern.