This paper presents an analytical study of organic contaminants transport in a cut-off wall and aquifer dual-domain system, considering the effects of the inlet boundary conditions and cut-off structural arrangements. The comprehensive sensitivity analysis of parameters focusing on the breakthrough time, attenuation time and cumulative concentration are presented using the Monte Carlo simulation and Sobol global method. The simplified constant inlet boundary condition can lead to an excessively conservative prediction of the contaminant breakthrough compared to the ‘finite mass’ and ‘decaying source’ boundary conditions. The cut-off wall hydraulic performance can be enhanced by reducing the contaminant's head loss, shape factor, half-life and cut-off wall hydraulic conductivity while increasing the retardation factor. The contaminant's half-life can largely influence the maximum contaminant concentration, attenuation time and breakthrough time. For example, the maximum contaminant concentrations for T1/2 = 1.4 years and T1/2 = 100 years are 13 and 123 times greater than that for T1/2 = 0.1 year, respectively. The influence of the variation of shape factor on the breakthrough curve should be taken into consideration. Altering the structural arrangement of the cut-off wall to accommodate a smaller shape factor increases the contaminant breakthrough time. The proposed solution allows the analysis of a cut-off wall and aquifer system with different inlet boundary conditions and structural arrangements of the cut-off wall.