According to the IUCN Red List of Threatened Species, North Island Hector's dolphins are "critically endangered" and South Island Hector's dolphins are "endangered". Hector’s dolphins are regularly caught in gillnets, which is by far the greatest threat to their survival. Small population size, segregated genetic groups, and low population growth rates (maximum plausible annual growth rate=1.8%) pose a significant threat to their persistence. Trawl nets, pollution, tourism, boat strikes and possibly mining are also thought to affect Hector's dolphins.

Between 1984 and 1988 a minimum of 230 Hector’s dolphins were killed in gill nets, and the majority of entanglements (91%) occurred during the spring and summer. The majority of by-catch occurs less than 4 nautical miles from shore, in water that less than 20 meters deep. Dolphins under 4 years old, particularly those under 2 years old, are caught in gill nets more often than older individuals. This suggests that younger dolphins may be less able to determine the presence of gill nets, possibly due to immature sonar systems. Dolphins under 2 years of age are usually with their mothers full time, however, after 2 years old they become more independent and may be more susceptible to gill net entanglement.

In 1988, the New Zealand Department of Conservation created the Banks Peninsula Marine Mammal Sanctuary under section 22 of the 1978 Marine Mammal Protection Act. The sanctuary is 1170 km², covering nearly 113 km of coast by prohibiting commercial gill netting within its boundaries year round and amateur gill netting from November to February. During all other months, amateur gill-netters are subject to regulations on where gill nets can be used. Despite this, commercial gill nets have been observed to be located on the sanctuary boundaries and amateur gill nets have been reported inside the sanctuary. In August 2001, a sanctuary on the west coast of North Island was established between Maunganui Bluff and Pariokariwa Point prohibiting gill netting. In 2008, the New Zealand Ministry of Fisheries submitted a proposal prohibiting gill netting along most of the east coast of South Island, 4 nautical miles from shore. Also in 2008, the Minister of Conservation proposed extending the Banks Peninsula Marine Mammal Sanctuary 45 km north and up to 12 nautical miles from shore. However, the Minister's proposal suggested removing gill net restrictions, focusing rather on limiting acoustic disturbances. As of 2009, both proposals were still under judicial review.

Hector’s dolphins are subject to bioaccumulation of PCBs and organochlorine pesticides, including dieldrin, hexachlorocyclohexane (HCH) and dichlorodiphenyltrichloroethane (DDT) and it’s metabolites (DDE and DDD). Dolphins on the east coast of South Island have 3 times higher concentrations of DDT and metabolites, and exhibit higher PCB levels than those on the west coast of South Island. The percent transfer of DDT and its metabolites from a mother to her fetus is 5.7%, and the transfer of PCBs to the fetus is 4.3%. Although it has not been documented, these numbers likely increase during nursing. Today DDT, DDE and DDD still persist in New Zealand soils, two decades after it was banned in New Zealand in 1989.

US Federal List: no special status

CITES: appendix ii

State of Michigan List: no special status

IUCN Red List of Threatened Species: endangered