This paper develops a qualitative causal model of a water, energy, and food (WEF) security nexus system to be used in analysing the interlinkages among those and other sectors that influence and are influenced by each other in a local context. Local stakeholder engagement through a group model building (GMB) approach was applied in Karawang Regency, Indonesia, to develop the model with the goals of improving problem understanding, raising consensus among participants, and building acceptance and commitment regarding the subsequent development of a quantitative nexus model. After recognizing the issues regarding water, energy and food sectors in the study area and eliciting opinions about nexus interactions, the next stage was to build a conceptual framework to describe the nexus system and to develop an integrated causal loop diagram (CLD) that describes critical system (inter-)linkages. The developed Karawang WEF security (K-WEFS) model is composed of six sub-models with water, energy and food sectors as endogenous factors. In addition, population, economic and ecosystem services were considered as exogenous drivers of the system. It is expected that all the major internal and external factors and drivers are covered, including possible feedback mechanisms, and key variables will be analysed further in the system. The future achievement of WEF security targets can be based on robust evaluation and planning processes underpinned by thorough understanding of whole system dynamics and the impacts of changes in the linked sectors, even in a qualitative way. In this way, a first step towards breaking silo thinking in regional planning may be attained.