Headwater catchments store valuable resources of quality water, but their hydraulic response is difficult to assess (model) because they are usually deprived of monitoring stations, namely hydrometric stations. This issue becomes even more pertinent because headwater catchments are ideal for the practice of conjunctive water resources management involving the supply of towns with groundwater and surface water, a solution that can be used to mitigate overexploitation of groundwater resources in densely urbanized and populated areas. In this study, a stepwise approach is presented whereby, in a first stage, a gauged basin was modeled for stream flow using the JAMS J2000 framework, with the purpose to obtain calibrated hydraulic parameters and ecological simulated stream flow records. Having validated the model through a comparison of simulated and measured flows, the simulated record was adjusted to the scale of an ungauged sub-basin, based on a new run of JAMS J2000 using the same hydraulic parameters. At this stage, a second validation of modeled data was accomplished through comparison of the downscaled flow rates with discharge rates assessed by field measurements of flow velocity and water column height. The modeled basin was a portion of Jequitiba River basin, while the enclosed sub-basin was the Marinheiro catchment (state of Minas Gerais, Brazil). The latter is a peri-urban watershed located in the vicinity of Sete Lagoas town, a densely urbanized and populated area. This town uses 15.5 hm3 year−1 of karst groundwater for public water supply, but the renewable resources were estimated to be 6.3 hm3 year−1. The impairment between abstraction and renewable resources lasts for decades, and for that reason the town experiences systemic water table declines and sinkhole development. The present study claims that the storage of quality water in the Marinheiro catchment, in a dam reservoir, would help alleviate the depletion of groundwater resources in the karst aquifer because this catchment could deliver 4.73 hm3 year−1 of quality surface water to the municipality without endangering ecologic flows. The construction of a small dam at the outlet of Marinheiro catchment could also improve aquifer recharge. Presently, the annual recharge in this catchment approaches 1.47 hm3 but could be much larger if the small dam was installed in the water course and the captured stream water managed properly.