Hydrosystems are important elements of the hydraulic cycle. With population growth and climatic change impacting water resources, the existing water transport systems need to be reproduced in order to optimize the usage of the precious water resources. The individual flow process i.e. unsaturated soil flow and groundwater flow in porous and fractured media can be expressed by partial differential equations mathematically. The numerical models are generally used to give solutions of these equations with specific conditions. In this work, the numerical solutions are carried out using the scientific software OpenGeoSys (OGS) based on the finite element method. The complex geometrical structure model domain can be imported into the numerical model with an implemented graphical interface. A GIS based relational database model GeoHydroDataBase (GHDB) designed to create a specialized set of geo- and hydro-objects is integrated with the numerical model. The multi-field and detailed computational hydrosystem analysis methodology is applied to Meijiang catchment and Nankou site respectively. As an application, the case study for the Meijiang area with the focus on surface/subsurface water interaction and the recharge response from surface infiltration to groundwater with different time series discretization. In the Nankou case study, a 3-D regional groundwater flow model is developed. The hydrogeological system is reproduced according to sparsely distributed boreholes data. The model calibration and sensitivity analysis are accomplished with inverse methods by applying a model independent parameter estimation system (PEST). The results of the calibrated model show reasonable agreements with observed water levels. The transient groundwater flow simulations reflect the observed drawdown of the last 9 years and show the formation of a depression cone in an intensively pumped area. The well calibrated 3-D groundwater model provides hydrogeological parameters and lateral fluxes from the adjacent mountain area for the following transport modeling and remediation scenarios analysis. In this study the method of capture zone type curves is used to estimate the pumping rate and the number of pumping wells needed for the contaminated aquifer cleanup. The analytical solutions of drawdown at the pumping wells (for both single pumping well and double wells) are compared with those calculated from the numerical model.