The presence of contaminants of emerging concern (CECs) in the aquatic environment has recently become a global issue. The very large number of CECs reported in the literature makes it difficult to interpret potential risks as well as the removal efficiencies, especially for the more recalcitrant compounds. As such, there is a need for indicator compounds that are representative of CECs detected in systems worldwide. In an effort to develop such a list, five criteria were used to address the potential for applying indicator compounds; these criteria include usage, occurrence, resistance to treatment, persistence, and physicochemical properties that shed light on the potential degradability of a class of compounds. Additional constraints applied included the feasibility of procuring and analyzing compounds. In total, 22 CECs belonging to 13 groups were selected as indicator compounds. These compounds include acetaminophen and ibuprofen (analgesic); erythromycin, sulfamethoxazole, and trimethoprim (antibiotics); diazepam and fluoxetine (antidepressants); carbamazepine (antiepileptic); atenolol and propranolol (β-blockers); gemfibrozil (blood lipid regulator); tris(2-chloroethyl)phosphate (TCEP) (fire retardant); cotinine (nicotine metabolite); atrazine, metolachlor, and N,N-diethyl-meta-toluamide (DEET) (pesticides); 17β-estradiol and cholesterol (steroids); caffeine (psychomotor stimulant); perfluorooctane sulfonate (PFOS) and perfluorooctanoic acid (PFOA) (surfactants); and iopromide (X-ray contrast agent). These thirteen groups of compounds represent CECs with the greatest resistance to treatment processes, most persistent in surface waters, and detected with significant frequency throughout the water cycle. Among the important implications of using indicator compounds are the ability to better understand the efficacy of treatment processes as well as the transport and fate of these compounds in the environment.