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• A 3D numerical model for canal seepage is established based on finite element method. • The model is calibrated and validated by ponding tests with four lining conditions. • The model is accommodated to concrete and geomembrane lining with cracks and holes. • The main factors influencing canal seepage under different scenarios are quantified. Concrete and geomembranes are common materials used in canal linings to decrease canal seepage. Current numerical studies focus on concrete linings only by equivalent continuous models and seldom are about geomembrane and are suitable to quantify the seepage loss from canals with damaged linings. In this study, a new model is developed for the coupled numerical simulation of seepage through concrete with cracks and a geomembrane with holes in canal lining damage based on the finite element method. In this model, the porous media is discretized into solid elements, whereas discrete cracks and geomembranes are modelled by zero-thickness elements, with the Richards equation and cubic law applied to describe the water seepage process. The porous media and crack zones are implicitly coupled in time and space through the exchange flow between the concrete and the crack zones in that the heads are integrated in a single matrix equation. The domain area is divided into two subdomain areas by the geomembrane. For the two subdomain areas, the surfaces of both sides in the geomembrane are treated as two flux boundaries. The proposed model is calibrated and validated by the results of ponding tests conducted on a canal with four lining treatments and additional experiments, which showed that the model fit the experiments very well. The model is applied to sensitivity analyses by varying the model parameters. The model is shown to be capable of simulating the seepage of canals lined by concrete and geomembrane lining with different cracks and holes. The sensitivity analysis shows that canal seepage mainly depends on the lining characteristics, such as the crack width, hole density, saturated hydraulic conductivity (K s) of the geomembrane, K s of the concrete, and K s of the soil layers adjacent to the canal bottom. [ABSTRACT FROM AUTHOR]