Large river water basins play a critical role in the economic, health, and biodiversity conditions of a region. In some basins, such as the Zambezi River Basin, extreme weather events introduce cycles of drought and heavy rainfall that can have extreme impacts on local communities vulnerable to environmental shifts. Annual flood pulse dynamics drive ecological dynamics in the system. In the dry season, water dependent wildlife in northern Botswana concentrates along the Chobe River- Floodplains. Elephant concentration, in particular, is matched to surface water quality declines. These flood pulse events have been linked to diarrheal disease outbreaks in the local population, the magnitude of which is associated positively with flood height. Modeling these interactions can advance our ability to predict events and develop mitigation and prevention actions. However, many challenges hinder this development including availability of data in regions that lack resources and the difficulties in create models for such large basins that account for overland water movement. This thesis presents work focused on addressing these challenges. Chapter 2 reports the development of a freely available Large Basin Data Portal (LBDP) that can be used to identify and create critical inputs for hydrodynamic models. This portal was used to create a hydrological model of the Upper Zambezi River Basin model (Chapter 3), a hydrodynamic model of the one of the three subbasins of the Zambezi River. The model was used to calculate downstream river discharges entering the Chobe-Zambezi Floodplains based on upstream rain events. The Upper Zambezi River Basin model was integrated with another more detailed model of the Chobe- Zambezi Floodplains (Chapter 4) that is designed to model the Chobe River and flood water movement in the floodplains. The models were created using the set of MIKE modeling software. The models were used to study various scenarios including water reductions that might occur due to climate change or drought and water increase that might be associated with extreme weather events. / Doctor of Philosophy / River water plays a key role in the livelihood of people and wildlife especially in region of the world suffering chronic economic challenges. The areas surrounding the Zambezi River in Africa is home to one of the most diverse ecological systems in the world. Extreme weather conditions bring cycles of drought and flooding especially in the Upper Zambezi region where wildlife, including the largest population of African elephants in the world, move closer to the Chobe River, a tributary of the Zambezi River, seeking water in the dry seasons. This research is focused on building a set of tools and models to enable studying the linkage between these events and aid in predicting the extent of the floods in the Chobe River Floodplain system based on rainfall in the Angolan high lands and other landscape features. Understanding how these dynamics are linked and the outcome in the downstream system provides a lead time for potential action.

Water is a primary shared resource that connects all species across the landscape and can facilitate shared exposure to a community of waterborne pathogens. Despite remarkable global progress in sanitation and hygiene development in the past two decades, infectious diarrhea remains a prominent public health threat in sub-Saharan Africa. This thesis identifies and discusses persistent challenges limiting the success of current waterborne disease management strategies and several existing research hurdles that continue to impede characterization of microbial transmission and transport. In this work, the Chobe River watershed in Northern Botswana serves as a target study site for the application of hydrological modeling tools to quantify emergent water quality and health challenges in Southern Africa. A watershed model with extensive data requirements, the Hydrological Simulation Program – Fortran (HSPF), is used to identify primary data gaps and model assumptions that limit the progress of model development, and guide opportunities for data collection, tool development, and research direction. Environmental pathogen exposure risk and epidemiological outbreak dynamics are best described by interactions between the coupled human and environmental processes within a system. The challenge of reducing diarrheal disease incidence strengthens a call for research studies and management plans that join multiple disciplines and consider a range of spatiotemporal scales. / Master of Science