The presence of pharmaceutical and hormone residues in water bodies is a matter of recent global concern. This study investigated the presence of such contaminants in two urban water bodies located in the city of Santa Maria, in southern Brazil. Two urban catchments, characterized by anthropogenic influences and poor household waste collection and treatment systems, were investigated. The Cancela-Tamandaí catchment covers an area of 2.7 km2, 50% of which is impervious soil, and is home to 14,300 inhabitants. The João Goulart catchment area covers 5.5 km2, 40% of which is impervious soil, and houses 11,900 inhabitants. Ten sampling campaigns were conducted in each catchment. Samples were checked for diclofenac, ibuprofen, paracetamol, 17 β-estradiol, estriol, ethisterone, estrone, and megestrol acetate. Four of the hormones (17 β-estradiol, estriol, estrone, and megestrol acetate) were not detected in either catchment. Ethisterone was detected in a single sampling campaign in Cancela-Tamandaí. Ibuprofen and paracetamol were detected in several samples, while diclofenac was absent. The mean concentration of ibuprofen in the João Goulart catchment was 0.51 μg L−1 and in the Cancela-Tamandaí it was 1.26 μg L−1. Mean paracetamol concentrations were 0.4 μg L−1 in the João Goulart catchment and 3.0 μg L−1 in the Cancela-Tamandaí.