The drainage systems of tunnels situated in limestone regions frequently encounter crystallization blockages. Numerous studies have addressed this issue, and their findings identified factors such as the flow velocity and temperature as influencing the crystallization process. However, these studies could not predict the occurrence of crystallization. Regarding theoretical approaches, most studies have focused on full-pipe operations or have solely considered flow-field dynamics without including simulations of the chemical reactions and mass transfers. This study introduces a mass-transfer model for drainage pipes based on a two-phase flow (water and air) with a free surface and non-full pipe flow that simulates the crystallization deposition process in drainage pipes. This model can predict the deposition conditions at varying flow velocities and intuitively visualize the crystallization process under the influence of various factors. The impact of flow velocity on the overall crystallization deposition process can be directly analyzed through simulations developed using this model. The results show that under conditions of incomplete pipe flow with no pressure at the outlet, the weight of the deposition first increases and then decreases within a certain velocity. This model can depict the variations within a 30 d period.