The complexity of local aquifers and the scarcity of the available data lead to consider different approaches for modeling specific groundwater flows. The proximity with lakes or retention basins, the interaction between groundwater, rivers and water bodies, heterogeneities into the aquifer contribute to increase the complexity. This paper focuses on the comparison of two different approaches, with the analytics elements method (AEM) and the well-known finite difference method (FDM), for the groundwater flow modelling. The AEM is based on a vectorial structure and the FDM on a raster structure. There is no competition between them. However, they can be more or less appropriated if we consider the spatial variability of the hydrosystem features and the resolution of the available data. They can also be used as two complementary approaches in a global way of simulation. In a global process of groundwater modeling, a good representation of the physical behaviour of the aquifer is necessary and decisive. Since the knowledge of the aquifer system must allow to identify and to formalize the hydrological features in a rigorous way, each model is combined with a GIS (Geographic Information System). An appropriate interface for the management of the modelization becomes available. The object oriented and vector representation of the Analytic Elements is an interesting alternative to the classical representation made with the FDM. This natural structure allows improving the interaction with the GIS, becoming more popular with the recent development of the computers technologies. Thus, it becomes efficient to well organize the geodatabase within a conceptual model to be well exploited by the numerical models. After recalling the global process of groundwater modeling, from the design of the conceptual model to the numerical results provided by the simulations, the paper focuses on the analysis of the approximations made and on the evaluation of the errors induced. This work focuses on a particular case study where groundwater resources management include gravel extraction, well for drinking water supplying and for irrigation. The area of interest is set in an alluvial aquifer along the banks of a major French river (the Loire River). This is a monolayer aquifer in an alluvial plain, which extends about 40 km along the river and about 6 km inside the major bed. This zone must take into account ecological constraints and foster the development of the fauna and flora in wetlands. Those wetlands are connected to the lagoons resulting from the previous gravel extraction. It requires the intimate knowledge of the hydrologic system and of the interactions between the aquifer, the lagoons, and the river. For each modelling methods, advantages and drawbacks are discussed.