While the Maloti-Drakensberg region is not generally associated with lakes, there are over 200 small, natural water bodies known as ‘tarns’ or pans, which occur from the foothills at around 1,600 m up to at least 3,000 m in altitude. These tarns are found from the Free State in the north, down through KwaZulu-Natal (KZN) and Lesotho to the Eastern Cape in the south. There are also dammed wetland lakes with evidence that larger water bodies were present before lake levels were raised, including Lake Letseng-la Letsie in Lesotho and Lake Matatiele in the Mountain Lake Nature Reserve near Matatiele in the Eastern Cape. Previous studies have demonstrated that Drakensberg tarns have extremely dilute waters with a very low buffering capacity which makes them extremely sensitive to acid deposition. Here we present evidence from the monitoring of precipitation chemistry at Cathedral Peak (KZN) and palaeolimnological studies of lake sediment records from Letseng-la Letsie and Lake Matatiele that industrial signals of contamination associated with coal-fired power stations are found across the region. High rainfall in the region and atmospheric recirculation patterns transporting pollutants from the Highveld mean that wet deposition fluxes of acidic sulphur and nitrogen compounds in the Maloti-Drakensberg may be among the highest in southern Africa. Furthermore, the great majority of tarns in the region are seasonal rather than permanent water bodies and hence likely to be extremely sensitive to the effects of climate change. Further studies are required to assess the magnitude of threats to the unique endemic biodiversity associated with tarns and lakes in the region.