The distribution of groundwater fluxes in aquifers is strongly influenced by topography, and organized between hillslope and regional scales. The objective of this study is to provide new insights regarding the compartmentalization of aquifers at the regional scale and the partitioning of recharge between shallow/local and deep/regional groundwater transfers. A finite-difference flow model was implemented, and the flow structure was analyzed as a function of recharge (from 20 to 500 mm/yr), at the regional-scale (1400 km2), in three dimensions, and accounting for variable groundwater discharge zones; aspects which are usually not considered simultaneously in previous studies. The model allows visualizing 3-D circulations, as those provided by Tothian models in 2-D, and shows local and regional transfers, with 3-D effects. The probability density function of transit times clearly shows two different parts, interpreted using a two-compartment model, and related to regional groundwater transfers and local groundwater transfers. The role of recharge on the size and nature of the flow regimes, including groundwater pathways, transit time distributions, and volumes associated to the two compartments, have been investigated. Results show that topography control on the water table and groundwater compartmentalization varies with the recharge rate applied. When recharge decreases, the absolute value of flow associated to the regional compartment decreases, whereas its relative value increases. The volume associated to the regional compartment is calculated from the exponential part of the two-compartment model, and is nearly insensitive to the total recharge fluctuations.