Application of Building Information Modelling (BIM) in architecture, engineering, and construction industry is known for its productivity and efficiency. Green BIM is one of the recent applications that aids users in achieving sustainability and/or improved building performance objectives through design and analysis of digital semantic models. The focus is on the application of green BIM for water efficiency (WE) analysis in accordance with the Malaysian Green Building Index (GBI) as a sustainability assessment tool. Revit Green Project Template (RGPT) and Autodesk Green Building Studio (GBS) as two available BIM tools were selected to evaluate and compare the applicability of each method for GBI WE assessment. To resolve the limitations identified from each evaluated method, automated GBI assessment tool (AGBIA) was developed as an alternative. The AGBIA as a supporting tool was established with the use of Dynamo, a visual programming tool to compensate for the limitations faced in the investigated methods. The practicality of each method was explored using a hypothetical model in Revit to automate information correspondent to 10 water efficiency assessment points and generate reports and documents necessary for the GBI design stage certification. The final phase involves verification of results obtained from each method using the conventional GBI WE calculator. AGBIA is suitable for the green BIM users in Malaysia based on the flexibility and automation over defining and assigning green parameters that are in line with the local context, the direct link of green information to the model, as well as the detail of presented data.