The world is undergoing rapid changes and the future is uncertain. The changes are related to modification of the landscape due to human activities, such as large and small scale irrigation, afforestation and changes to the climate system. Understanding and predicting hydrologic change is one of the challenges facing hydrologists today. Part of this understanding can be developed from observed data, however, there often too few observations and those that are available are frequently affected by uncertainties. Hydrological models have become essential tools for understanding historical variations of catchment hydrology and for predicting future possible trends. However, most developing countries are faced with poor spatial distributions of rainfall and evaporation stations that provide the data used to force models, as well as stream flow gauging stations to provide the data for establishing models and for evaluating their success. Hydrological models are faced with a number of challenges which include poor input data (data quality and poorly quantified human activities on observed stream flow data), uncertainties associated with model complexity and structure, the methods used to quantify model parameters, together with the difficulties of understanding hydrological processes at the catchment or subbasin. Within hydrological modelling, there is currently a trend of dealing with equifinality through the evaluation of parameter identifiability and the quantification of uncertainty bands associated with the predictions of the model. Hydrological models should not only focus on reproducing the past behaviour of a basin, but also on evaluating the representativeness of the surface and subsurface model components and their ability to simulate reality for the correct reasons. Part of this modelling process therefore involves quantifying and including all the possible sources of uncertainty. Uncertainty analysis has become the standard approach to most hydrological modelling studies, but has yet to be effectively used in practical water resources assessment. This study applied a hydrological modelling approach for understanding the hydrology of a large Tanzanian drainage basin, the Great Ruaha River that has many areas that are ungauged and where the available data (climate, stream flow and existing water use) are subject to varying degrees of uncertainty. The Great Ruaha River (GRR) is an upstream tributary of the Rufiji River Basin within Tanzania and covers an area of 86 000 km2. The basin is drained by four main tributaries; the Upper Great Ruaha, the Kisigo, the Little Ruaha and the Lukosi. The majority of the runoff is generated from the Chunya escarpment, the Kipengere ranges and the Poroto Mountains. The runoff generated feeds the alluvial and seasonally flooded Usangu plains (including the Ihefu perennial swamp). The majority of the irrigation water use in the basin is located where headwater sub‐basins drain towards the Usangu plains. The overall objective was to establish uncertain but behavioural hydrological models that could be useful for future water resources assessments that are likely to include issues of land use change, changes in patterns of abstraction and water use, as well the possibility of change in future climates.