An important leakage risk associated with CO2 geological sequestration is the potential transport and fate of organic contaminants due to the CO2 leakage. In this paper, a precipitation and deposition dynamic model was constructed using COMSOL to evaluate the potential impacts of organic contaminants in response to the leakage of CO2 and brine into a shallow aquifer. The Span-Wagner equation and Peng-Robinson equations were adopted to estimate the partitioning behavior of organic contaminants. Numerical simulations with naphthalene as a representative contaminant show that the dissolved component is transported with the equilibrium concentrations at the thermodynamic conditions built by the fluid phase, while the precipitated solid particles are either transported with carrier fluid or deposited in the leakage pathway according to the deposition dynamic model. The sharp decrease of solubility promotes the precipitation impetus while the deposition rate mainly depends upon the leakage velocity and pore structure. Local blockage may occur due to the accumulation of deposited particles, and the potential location is most likely to be near the outlet of the leakage pathway in current scenario. Sensitivity analyses indicate that pressure difference and temperature buildup would influence both the leakage velocity and deposition dynamics, while the pore structure of leakage pathway, represented by porosity and permeability, will affect the leakage characteristic so as to the deposition rate. The presented models are generic in nature for naphthalene transport, demonstrating a methodology that can explore the generation of a potential third organic phase in contaminant transport for risk assessments.