A groundwater resources assessment has been carried out for the Lake Nyasa Basin east Africa, with reference to sub catchments further to the whole basin wise analysis, including quantification of potential yields from the aquifers. Numerical groundwater models, MODFLOW-SURFACT coupled with Visual MODFLOW, were used to assess sub-basin groundwater sustainability (Via “Zone Budget” software package). The model has been calibrated to observed hydraulic head and processed baseflow estimate. It is concluded that the aquifer system is sustained by episodic recharge and the long-term gaining storage which represents the maximum extractable volume. Future predictions of groundwater usage indicate that by 2035 the percentage of annual safe yield extracted will increase to between 11.3 and 103%. Model result suggests that there is a need to revise the current estimate of sustainable yield based on future climate change conditions and projected population growth, which would decrease spring flows substantially and decrease hydraulic head basin-wide. It also suggests that by 2035 some sub catchments will be nearly at or exceeding the annual safe yield leaving no room for socio-economic development, or the need to reduce existing socio-economic demands to meet domestic demands. Besides to improving the natural replenishment capacity through artificial recharge technique, the other option is to increase the percentage of total recharge allocated to the annual safe yield from 10% of the total annual recharge to 20% in these catchments. This provides a basis for management of individual groundwater scheme in sustaining livelihood activities or implications of policies and to develop a plan for potential groundwater extraction scenarios pertaining to water use and allocation.