The purpose of this study is to present the development and application of residual flow procedure for analysis of three-dimensional (3-D) steady-state and transient seepage. The finite element equations are derived using a pseudo-variational principle which leads to a transient residual flow (load) vector that, in turn, is used to correct the position of the free surface iteratively. The procedure involves a fixed mesh which requires no mesh regeneration during transient analysis and during iterations. The procedure is also capable of handling material nonhomogeneities and anisotropy with relative ease. Several applications are made including verification with respect to closed-form solutions, and with results from a laboratory glass bead model simulating three-dimensional situations. For these glass beads, the coefficients of permeability and specific storage are also evaluated experimentally.