Despite advances in water resources management and planning, the São Francisco River Basin in Brazil has suffered from systematic drought problems in recent years, leading to severe human and environmental water security threats. This paper aims to track the water security for different periods and its relations with the changes in physical and natural asset conditions. The paper explores how investment planning to mitigate the water security threats and explore opportunities to increase the value of investments. The paper finds that grey infrastructure has regulated threats from increasing in the downstream of the river basin, however, continuous increase in water security threats in the upstream of the basin threatens water security downstream. This is evident from the spatial connectivity and unidirection externalities. As the capacity to further increase in grey investment is reaching its limit in the downstream, the increases in green infrastructure investment upstream, especially in the Grande River basin, could be one the way to reduce the externalities and minimise the water security risks.