Wastewater treatment plant (WWTP) is a sustainable technique for making wastewater reusable for non-potable purposes. However, in developing countries, most conventional WWTPs are not equipped to trap all pharmaceutical residues (PRs) and pharmaceutically active chemicals (PhACs). This study aims to perform non-target screening of these contaminants in wastewater and explore health and environmental hazards and the removal efficiency of a WWTP in Malaysia. At Indah Water WWTP, a total of 28 wastewater samples (i.e., 2 L each of 14 influent and 14 effluent) were collected every day for a week from February to April 2023. The supernatant of the centrifuged sample was analyzed with the LCMS-QTOF system. Chromatographic profiles were analyzed, and the compounds were annotated using the METLIN database. Categorical data were statistically analyzed with SPSS 29.0 using a chi-square test and continuous variables using paired t-test and multiple regression. PRs like micronutrient (9, 2.3%) and PhACs like lipid (83, 20.8%) were more frequent. Detection frequencies of PRs and PhACs were 72 (18%) and 328 (82%), respectively. Efficiency of WWTP was 36.4 to 100% for PRs removal (mean ± SD: 65.85 ± 56.43%) and 20 to 100% for PhACs removal (mean ± SD: 49.30 ± 55.94%). A total of 943 (mean ± SD: 67.36 ± 43.28) and 400 (mean ± SD: 28.57 ± 32.44) unique PRs and PhACs were recorded. A total of 40 (10%) PRs and PhACs had the potential to irritate eyes, skin, and respiratory tract, and 46 (11.5%) chemicals needed to be avoided from being discharged into the environment. Though WWTP was 98.0% compliant with environmental standards, its efficiency should still be increased to remove the full range of PRs and PhACs. The research has implications for SDGs 6 and 14.