Intense urbanisation in many coastal areas has led to intensification of groundwater consumption, while reducing permeable areas and increasing the frequency and magnitude of flooding. Among the potential strategies to compensate for these adverse effects, which are expected to become worse as a result of climate change, rooftop rainwater harvesting (RWH) in combination with managed aquifer recharge (MAR), may be indicated. This work investigated the performance of different configurations of such a system, tested as a twofold sustainable stormwater and domestic water management tool in a tropical metropole (João Pessoa, Brazil). This area located over a sedimentary aquifer system illustrates the water security challenges of densely urbanised areas in southern cities. To that end, several configurations of rooftop catchments and storage volumes were evaluated, by simulating a MAR-RWH system connected to the regional unconfined aquifer (Barreiras Formation) through a 6″ diameter injection well. Rainfall-runoff-recharge processes and water balances were simulated using monitored high-temporal resolution rainfall data. The results showed that catchments ranging from 180 to 810 m², connected to tanks from 0.5 to 30.0 m³, are the optimal solutions in terms of efficient rainwater retention and peak flow reduction. These solutions provided mean annual estimates of aquifer recharge between 57 and 255 m³/yr from 2004 to 2019. The results of this study highlight the opportunity for MAR schemes to reconcile stormwater management and water supply goals.