About 3.0 million people living under a typical tropical savannah climate in the Brazilian Federal District (FD) have faced an unprecedented water crisis. Considering the need for indirect reuse of wastewater for public supply, this work aimed to investigate FD water sources regarding the presence and risks of three contaminants of emerging concern: caffeine, carbamazepine, and atrazine. Samples from two current water sources (Descoberto and Santa-Maria Lakes) and two future water sources of the FD (Paranoá and Corumbá Lakes) were analyzed by solid-phase extraction followed by liquid chromatography coupled to hybrid quadrupole-time-of-flight mass spectrometry (UPLC-QTOF/MS). Method precision and accuracy were satisfactory and limits of quantification ranged from 0.37 to 0.54 ng/L. Higher concentrations were observed for caffeine in the future water sources (39 to 180 ng/L) followed by carbamazepine (5.4 to 25 ng/L) and atrazine (3.9 to 15 ng/L). The less-impacted water sources, in current use in the FD, present caffeine concentrations ranging from 4.8 to 32 ng/L and atrazine levels varying between 2.4 and 5.5 ng/L. Carbamazepine was not detected in these reservoirs. Environmental risk assessment indicates a possible risk for carbamazepine and atrazine, evidencing the need for further studies. No human health risk was depicted within the results.