In the beginning of the war the Herero, under the leadership of chief Samuel Maharero had the upper hand. With good knowledge of the terrain they had little problem in defending themselves against the Schutztruppe (initially numbering only 766). Soon the Namaqua people joined the war, again under the leadership of Hendrik Witbooi.
To cope with the situation, Germany sent 14,000 additional troops who soon crushed the rebellion in the Battle of Waterberg in 1904. Earlier von Trotha issued an ultimatum to the Herero, denying them citizenship rights and ordering them to leave the country or be killed. In order to escape, the Herero retreated into the waterless Omaheke region, a western arm of the Kalahari Desert, where many of them died of thirst. The German forces guarded every water source and were given orders to shoot any adult male Herero on sight. Only a few of them managed to escape into neighbouring British territories. These tragic events, known as the Herero and Namaqua Genocide, resulted in the death of between 24,000 and 65,000 Herero (estimated at 50% to 70% of the total Herero population) and 10,000 Nama (50% of the total Nama population). The genocide was characterized by widespread death by starvation and from consumption of well water which had been poisoned by the Germans in the Namib Desert.[10][11][12]