Climate change is driving increased variability in precipitation patterns across much of southern Africa, making it challenging to model catchment-scale water dynamics using historical data. This has implications for effective water management particularly in water scarce areas which have competing users. Agriculture is an important water user which lacks detailed records of surface and water abstraction, making it difficult for hydrological models to replicate catchment water balances required for effective management. This study takes a fully distributed hydrological model (J2000), which was initially developed to model virgin streamflow, and incorporates remote sensing evapotranspiration to understand the impact of irrigation on both streamflow and baseflow. The model was developed for the RAMSAR listed Verlorenvlei estuarine lake, South Africa. Recent drought in the region has shown that understanding low-flow conditions is critical to the long-term ecological sustainability of the lake, but the lake catchment is also an important agricultural region that competes for scarce water resources. The J2000 model developed to model recharge and aquifer baseflow through a coupled approach and has here been modified to incorporate remote sensing estimates of evapotranspiration to quantify streamflow reduction. The irrigation package of the J2000 was firstly modified to satisfy the remote sensed ET demand using the modelled streamflow during the wet months of the year. During low flow conditions (dry months), the irrigation package was instructed to utilise stored groundwater from either the primary or secondary aquifer or both based on the abstraction position within the sub-catchment. The results of the study show that the streamflow reductions are significant in this sub-catchment and that if agricultural expansion continues there will not be enough water to support the high biodiversity levels of the Verlorenvlei. While the impact of climate change on rainfall in the region has not been incorporated into the model structure as of yet, it is expected that there will be a reduction in rainfall into the future, which will further impact the systems’ ability to handle sustained periods of low flow conditions. The methodology used in this study can be transferred to other semi-arid catchments which lack sufficient streamflow estimates to guide effective water management and limit the over allocation of water resources for socio-economic development and poverty alleviation.