Kinematic boundary condition is usually used when dealing with transient free-surface flow problems in isotropic media. When dealing with anisotropic problems, a transformation can transform the anisotropic media to an equivalent isotropic media for seepage analysis, but the kinematic boundary condition cannot be used directly in the transformed media. A generalization of the kinematic boundary condition along any arbitrary direction is derived for use in the transformed domain for general three-dimensional anisotropic problems. A boundary element method for solving transient free-surface seepage problems is developed and the treatment of the proposed kinematic boundary condition in the boundary element method is given. Three examples have been solved to show the reliability and flexibility of the model. Examples are verified with some available experimental and numerical cases to show the accuracy of the model for predicting the phreatic surface and it is shown that anisotropy has a very important and non-neglecting effect in the behavior and the shape of phreatic surface.