Fractures can have significant influence on water flow and solute transport in geological bodies as well as the management of underground water. It is important to develop a model that can accurately and efficiently simulate water flow within fracture networks, porous media and fractured porous media. The present study focuses on the grouping of fractures, representation of fracture networks, high quality mesh generation of2D/3D fracture networks and dual media, water flow analysis in discrete fracture networks, porous media and dual media.Above all, the water flow analysis method, the Topological Pipe Network Method (TPNM), is proposed for water flow simulation currently being developed using MATLAB. It is considered to simulate water flow in both an efficient and accurate manner, and to unify discrete fracture networks and continuous porous media with a discrete pipes network. It is conceptually and computationally different from traditional methods.(1) An enriched K-means clustering method for the grouping of fractures with meliorated initial cluster centers is proposed. The concept of gather degree, hierarchical method and Xie-Benni validity index are integrated to enrich the traditional K-means method. Case studies show that the enriched K-means method alleviates the sensitivity from the adopted threshold value and produces relatively consistent results with various threshold values. The algorithm exhibits good clustering capabilities.(2)2D/3D fracture networks are modeled which can replicate not only the conceptual models proposed in literature, but also fractures in any2D convex polygonal shape with infinite or finite sizes. Both2D/3D connectivity analyses are carried out based on the graphical connection relationships of fractures and boundaries. The connectivity analysis of2D and3D fracture networks are unified and degenerated into a2D network analysis. Tree cutting algorithms for water flow analysis are also implemented based on the connectivity analysis.(3) An enriched meshing method of2D dual media and3D fracture networks are proposed. A constrained Delaunay method and a distance-based density function are integrated and embedded into the enriched meshing method of dual media which can generate fine and gradually changing meshes around fractures. Meshing of3D fracture networks is innovatively degenerated into a2D problem. This procedure not only simplifies the problem itself, but also makes it possible to produce high quality meshes in complex3D fracture networks.(4) TPNM is proposed for water flow analysis in discrete fracture networks, porous media and dual media. It is conceptually and computationally different from conventional water flow simulation methods. Conceptually, the continuous porous media and the discrete fracture networks are unified in a discrete manner and degenerated into a topological pipes network. A2D or3D problem is simplified into a1D problem, which significantly improves the computational efficiency. Computationally, TPNM is proposed based on the topological interpretation of the physical model and the corresponding governing equations. All equivalent parameters are analytically derived, which avoids over simplification and ensures high accuracy. In addition, TPNM is demonstrated with high accuracy by comparing with analytical solutions and that from commercial software, such as the Universal Distinct Element Code (UDEC) and the COMSOL Multiphysics. Case studies also indicate that the proposed method has the potential to be extended to other thermo-mechanical-hydraulic coupling problems.