Because some problems could not be resolved, such as singular points, inhomogeneous media, unconfined aquifer, etc, applications of the boundary integral equation method (BIEM) to engineering? even to seepage simulation and management in porous media, get seriously influenced. In order to promote widely its applications, some improved projects have been developed and applied to practice aiming at the key techniques. (1) Problems of inhomogeneous media and unconfined aquifer could be completely solved by infinite series approach methods in implement of BIEM. It is shown by the case studies that the methods not only take full advantages of traditional BIEM, but also overcome effectively its deadly disadvantages and get enough accuracy. It should be used at suitable conditions; (2) Accuracy of BEM can be convinced by singular point treatment and 'double nodes one value method' is the best one in all methods; (3) It is shown by solving dewatering practice in a surface mine that compared with the embed method, the response matrix method has advantages of full using inherence relationship in hydraulic system, smaller restrict condition matrix, rapidly calculation. Combined with response matrix method, Laplace transform of BIEM can even more develop advantages of dimensional reduced in solving, being independent of time steps, less workload, excellent accuracy.