An uncontrolled rapid filling or discharging of a pipeline can create compressed air columns in an urban water supply or sewage system. The expulsion of entrapped air out of pipelines is considered as one of the most destructive phenomena. Generally, the air valves are mounted and used to release the air from the pipe. Any failure of the air venting system may lead to a pressure surge inside the pipeline and even damage to the water systems infrastructure. Most of the investigations of multiphase flow during a rapid filling are limited to small distribution systems due to high computational costs. The aim of the present research is to develop a 1D-3D coupled model with the capability to handle multiphase flows. The effects of air pocket length, orifice size and upstream pressure on the flow field and maximum pressure surge inside the pipe are investigated. The classical water hammer equations are solved for the 1D domain using the Godunov scheme while the rest of the system is simulated using the Volume of Fluid (VOF) method. The coupling between 1D and 3D domains are handled using the developed boundary conditions based on flow characteristics. The results of the numerical simulations are compared with available experimental data. The obtained results show that the model can predict the features of the two-phase flow inside the pipeline during a rapid filling. The required computational time decreases by a factor of 4 compared to 3D simulations. This gives the possibility to investigate large scale water distribution or drainage systems.