Major threats to the ecosystems in the Kunene River Basin vary between the different ecoregions.
Generally, large areas of the ecoregion are sparsely settled. Habitat fragmentation and modification through settlement and agriculture are relatively limited. Consequently, human impacts to biodiversity are low at the present time. This can change in the future if the numbers of farmers or farm size increases or mining companies exploit the area. Since the regional ecology is poorly studied, the real impact at present is not clear. This leaves much space to conduct further studies.
The aftermath of the Angolan civil conflict is one of the main reasons for biodiversity damage in the whole region. It led to poor security, economic depression, lack of infrastructure and basic services as well as a massive displacement of rural populations.

Clearing of forest for preparation of arable land in Upper Kunene basin.
Source: Tump 2008
( click to enlarge )
The main existing threats to biodiversity are:
-
Formerly displaced rural people return to their farming areas. Encroachment of subsistence agriculture in the fertile escarpment forest areas of the upper Kunene has become a major threat to biodiversity.
-
Logging and harvesting of forest products is the greatest threat to forest areas in the upper and middle Kunene.
-
Flow control through building Dams and Extraction of Water has a potentially negative impact on biodiversity.
-
Hunting - for subsistence or for valuable body parts of some species - is ongoing nearly uncontrolled in many regions of Angola, including protected areas. The insecure situation hinders the management of protected areas and the prevention of poaching.
-
Invasive alien species can out-compete indigenous organisms.
-
Park borders, international boundaries, and human settlements particularly along the river block annual migration routes of animals.
-
Cross-border smuggling of wildlife products in areas where security levels are low is a major concern for wildlife management and protection.
-
Off-road driving threatens the sensitive environment in the desert parts of the Lower Kunene River basin (Kaokoveld).