This study provides the first set of quantitative data on the occurrence and fate of a wide range of contaminants of emerging concerns (CECs) in Indonesia’s largest wastewater treatment plant (WWTP). The WWTP employs waste stabilization ponds (WSPs) as the secondary treatment before discharging the effluent to the Citarum River. Fourteen out of twenty-two monitored CECs were detected in the wastewater influent, and seven were present in the effluent, with a total concentration of 29.8 ± 0.4 µg/L and 0.5 ± 0.0 µg/L, respectively. The occurrence of the CECs in this study was found to be well correlated with their possible use and known detection in surface waters in Indonesia. Caffeine (CAF) at 12.2 ± 0.1 µg/L, acetaminophen (ACT) at 9.1 ± 0.1 µg/L, N,N-diethyl-m-toluamide (DEET) at 5.0 ± 0.1 µg/L, ibuprofen (IBU) at 2.3 ± 0.0 µg/L, and triclosan (TCS) at 470 ± 64 ng/L were discovered as the five most prevalent CECs, followed by bisphenol A (BPA), trimethoprim (TMP), Tris(2-chloroethyl) phosphate (TCEP), sulfamethazine (SMZ), carbamazepine (CBZ), fluoxetine (FLX), benzotriazole (BTA), sulfamethoxazole (SMX), and metformin (METF). Biodegradable CECs (SMX, SMZ, ACT, IBU, TCS, BPA, CAF, DEET, and TMP) were efficiently removed (83–100%) by the WSP. In contrast, recalcitrant CECs achieved poor removal efficiencies (e.g., FLX at 24%), and for others, treatment processes even resulted in elevated concentrations in the effluent (CBZ by 85%, TCEP by 149%, and BTA by 92%). The CECs’ influent concentrations were determined to pose a moderate aquatic cumulative risk, while no such risk was associated with their effluent concentrations. The study demonstrates the importance of conventional WWTPs in reducing the concentrations of CECs to minimize their aquatic contamination risk. The findings are relevant for countries, such as Indonesia, with limited resources for advanced centralized wastewater treatments, and which are exploring the efficacy of centralized WSP against the existing decentralized treatments.