Seepage flow through complex foundations is one of the main factors causing dam failure. To foresee this problem, seepage modeling and analysis are usually performed. This study investigated seepage behavior as affected by complex, foliated, rock foundations in an earth dam. The PLAXIS 3-D LE software was used to analyze seepage problems for steady state flow. The normal high-water level (NHWL) with anisotropic permeability was considered in the models. The anisotropic permeability of foliated rocks was determined according to the angle of inclination. The flow characteristics along the dam axis could be divided into five zones, with three zones for the middle parts (MD1, MD2 and MD3) and one zones for each of the two abutments (LA and RA). The quantities of flow (water transmissibility) upstream to downstream (QX) on each zone highly depended on the geological structures. Although the average seepage transmissibility values of the residual soil and phyllite were almost equal for every zone. The values in the anticline areas were higher than for the syncline areas, especially for the middle zones. The flow tended to transfer from residual soil into phyllite rock in the anticline area. The transmissibility ratio of anticline to syncline was more than 2 times for both the residual soil and phyllite. The finger drain and river channel attracted substantial flow in the longitudinal (QY) and vertical (QZ) directions. However, the verification of the field piezometric versus the modeling heads showed the possibility of blockage of the finger drain.