The purpose of the paper is to provide an analysis of sustainability issues related to the practical implementation of the concept of basin management with reference to the Karst Water Management Body (KWMB) in Namibia. A river basin is regarded as an appropriate management unit and the concept of establishing basin management institutions was introduced to achieve the objectives of sustainable natural resources management in general. However, the karst aquifer is unique because it lies in the headwaters of a number of river basins and the management of this groundwater resource goes a little beyond the logic of water resource management as it is understood for surface water sources. In view of the unacceptability of the perceived top down management of water resources, a need was identified for a participatory approach to integrated groundwater resources management in the Otavi Mountain Land in Namibia. After consultations with the Government of Namibia (Government), the KWMB was established to assist stakeholders who obtained water for domestic use, mining and irrigation from aquifers in a karstified hydrogeological environment located in the Otavi Mountain Land in northern Namibia with the management of their water sources. The karst area has been declared a groundwater control area by the Government and provides the framework for efficient and sustainable management of groundwater resources. The eventual sustainability of a basin management institution depends on the justification for such an institution, the capacity of the stakeholders to drive the required activities, the resources at the disposal of the institution and numerous other factors beyond the control of the institution. The paper discusses the practical application of the principles and concepts of basin management, the challenge of stakeholder participation, the impact of Government policy and legislation as well as the sustainability of the basin management institution. The paper demonstrates that management of surface water basins and groundwater aquifers are different in nature and require different management approaches. Keywords: Aquifer management, Basin management, Groundwater allocation, Stakeholder participation.