The 2003 drying of Zibadianja Lagoon (and its reserve) situated on the south of Kwando-Linyanti Rivers in Botswana had negative impacts on the tourism in the concession area operated by a commercial tour operator. Aerial surveys and extensive ground studies were undertaken to investigate the factors responsible for reduced flows into the lagoon. Fifteen years hydrometric data collected in the Kwando and Linyanti Rivers were used to substantiate the changing flood regimes into the lagoon. The inflow channels to the lagoon with extensive blockages were identified and water flow measurements in the channels were determined on monthly basis before and after the clearance of blockages. The flow measurements and monitoring indicated that the water flow reductions in the Kwando River over a time scale, the development of vegetation blockages in the supplier channels, wildlife grazing and rising of sediments facilitated the drying of the Zibadianja lagoon. The feeder channels to the lagoon had been continuously monitored and managed to restore the hydrology and to rehabilitate the ecosystem in the area, which has improved the tourism activities.