Estimation of groundwater flow in a sub-regional area commonly fails to consider both vertical exchange across the boundary between flow systems of different hierarchy, and flow exchange between topographic basins. Components of the groundwater-balance in thick, fractured aquifer units in most areas, should include: 1) contributions from considerable depths, as well as from 2) adjacent units, 3) rainfall, 4) irrigation, 5) abstraction, and 6) change in storage. Early aquifer studies ignored vertical flow from depth as it was assumed to be negligible. However, often such flow is significant, in terms of available resources, to affect both water temperature and chemistry during abstraction. The use of the groundwater-budget method in a semi-arid drainage basin in San Luis Potosí, Mexico, where horizontal flow is assumed to prevail, raises two major questions: A) is the aquifer been improperly labeled as "overexploited" in terms of water availability (i.e., rate of lateral inflow is 20 times less than total abstraction rate), thus preventing additional development? and (B) is upward vertical component of deep groundwater flow significant in terms of the water budget? Contributions 2, 3 and 4 are nil in the analyzed confined aquifer. Storativity values (<0.002) suggest that capture, natural-discharge reduction, and enhancement of vertical regional inflow, or a combination of these, sustain groundwater abstraction estimated in about 2.6 m3/s. The differences between abstraction and horizontal inflow erroneously suggests that groundwater is developed beyond an extent where outflows are larger than inflows. If abstracted groundwater were from storage, the change in storage (about -1.3 m/annum) would have to be much greater to account for the water needed to meet abstraction; errors in the estimated abstraction are not enough to explain that difference. Hence, regional, sustainable, economic development in the basin has been constrained due to an inferred negative groundwater balance. However, recent hydrogeological modeling suggested an inter-basin vertical upward inflow of about 1.8 m3/s is to be considered in a regional management approach. This inflow could contribute to a sustainable development if its fluoride content of up to 3.6 mg/l is controlled by abstraction strategies.