Earlier investigators have numerically carried out performance analysis of the invert trap fitted in an open channel using the stochastic discrete phase model (DPM) by assuming the open channel flow to be closed conduit flow under pressure and assuming zero shear stress at the top wall. This is known as the fixed lid model. By assuming the top wall to be a shear free wall, they have been able to show that the velocity distribution looks similar to that of an open channel flow with zero velocity at the bottom and maximum velocity at the top, representing the free water surface, but no information has been provided for the pressure at the free water surface. Because of this assumption, the validation of the model in predicting the trap efficiency has performed significantly poorly. In addition, the free water surface subject to zero gauge pressure cannot be modeled using the fixed lid model because there is no provision of extra space in the form of air space for the fluctuating part of the water surface profile. It can, however, be modeled using the volume of fluid (VOF) model because the VOF model is the appropriate model for open channel or free surface flow. Therefore, in the present study, three-dimensional (3D) computational fluid dynamics (CFD) modeling with the VOF model, which considers open channel flow with a free water surface, along with the stochastic DPM, was used to model the trap efficiency of an invert trap fitted in an open rectangular channel. The governing mathematical flow equations of the VOF model were solved using the ANSYS Fluent 14.0 software, reproducing the experimental conditions exactly. The results show that the 3D CFD predictions using the VOF model closely fit the experimental data for glass bead particles.