Climate change and anthropogenic factors' impact on habitat loss is a growing problem that is influencing unsustainable wildlife local-population home range shifts and triggering an increase in human–wildlife conflict (HWC). Yet, keystone species involved in HWC such as elephants play a vital role in nature-based ecosystem services and have important economic and cultural value to the people that are living with them. To understand how climate change and anthropogenic factors affect habitat loss and elephants’ home range shift, the movement of Namib desert-dwelling elephants was monitored and observed in the Ugab River basin between February 2018 and November 2020 at fortnight intervals. There are 87 elephants in the Ugab River basin that are distributed into two subpopulations: desert-dwelling elephants (N = 28) and semi-desert-dwelling elephants (N = 59). To achieve the objective of the study, land cover change, elephant movement, rainfall, and temperature data were analysed using ArcGIS spatial and statistical tools, such as image analysis, optimised hot spot analysis (OHSA), and cost distance analysis, to distinguish habitat vegetation changes and home range shifts and how these link to emerging human–elephant conflict (HEC) hot spots. Human farming activities, poor rainfall, and frequent droughts are responsible for the loss of habitat of around 73.0% in the lower catchment of the ephemeral river streams; therefore, the urgency of conserving and sustaining these habitats and desert-dwelling elephants is discussed here. Keywords: desert-dwelling elephants, home range shift, habitat loss, Namib Desert, ephemeral rivers, vegetation cover, NDVI, human-elephant conflict.