Water shortages across the globe have increased due to climate change among other factors with negative impacts expected at the river basin level. Anticipating these impacts will help experts act in a timely manner to avoid a future water crisis. As part of addressing the future water shortage impacts on the Togolese community, this paper assessed water security in the context of the global environmental change in the Oti River Basin taking Oti Nord sub-basin (ONSB) as a case study. Key informants’ interviews were done with staff from governmental institutions, Non-Governmental Organizations (NGOs), community-based organizations, and private operators. The Improved Fuzzy Comprehensive Evaluation Model (IFCEM) was used for assessing water security (WS). A basin level WS evaluation system including five subcomponents (external environment security, water resources security, water-society security, water economic security, and water-environment security) and 23 indicators related to climate, socio-economy, water availability, and consumption were constructed. The results showed that the water level is very insecure in the sub-basin for the assessed years (2010, 2015, and 2025) with the year 2025 being the worst (expected a decrease of water security by 20% and 1% in 2025 compared to the years 2015 and 2010, respectively). This insecurity is found to be the result of many factors including technical, institutional, juridical, environmental, socio-cultural, hydrogeological, and demographical factors. However, managerial factors such as institutional instability, the inadequacies in water and related sector evolution, and the absence of de-centralized water management structures, the non-operationalization of management organs/financial instruments, and culture (i.e., taboos and bylaws) are found to be key to the study area. The paper concluded that the operationalization of management organs/financial instruments may enable the application of adopted water policies and regulations, which may lead to a sound and coordinated management of the available water resources since this will enable the government’s self-investment in clean water provision, data acquisition (potential water available and the estimation of economic driven potential water needs, which are key for any sound development), and a stimulated joined effort from the existing institutions. In addition, the establishment of a sound waste management system and awareness raising, and educative activities regarding water pollution will be of great benefit for this cause.