This work investigates the influence of ammonium ions and the organic load (chemical oxygen demand (COD)) on the UV/chlorine AOP regarding the maintenance of free available chlorine (FAC) and elimination of 16 emerging contaminants (ECs) from wastewater treatment plant effluent (WWTE) at pilot scale (UV chamber at 0.4 kW). COD inhibited the FAC maintenance in the UV chamber influent at a ratio of 0.16 mg FAC per mg COD (kHOCl–COD = 182 M−1s−1). An increase in ammonium ion concentration led to a stoichiometric decrease of the FAC concentration in the UV chamber influent. Especially in cold seasons due to insufficient nitrification, the ammonium ion concentration in WWTE can become so high that it becomes impossible to achieve sufficiently high FAC concentrations in the UV chamber influent. For all ECs, the elimination effect by the UV/combined Cl2 AOP (UV/CC) was not significantly higher than that by sole UV treatment. Accordingly, the UV/chlorine AOP is very sensitive and loses its effectiveness drastically as soon as there is no FAC but only CC in the UV chamber influent. Therefore, within the electrical energy consumption range tested (0.13–1 kWh/m3), a stable EC elimination performance of the UV/chlorine AOP cannot be maintained throughout the year.