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The Káraný waterworks supplies drinking water to about one-third of Prague, the capital city of the Czech Republic with a population of more than 1 million. The combination of two technologies—bank infiltration and artificial recharge—are used for production of drinking water. The two-year monitoring of PPCPs (pharmaceuticals and personal care products) at monthly intervals observed temporal changes in 81 substances in the source river and groundwater, and the efficacy of contamination removal depended on the treatment technology used. The results showed a very wide range of PPCPs discharged from the waste water treatment plant at Mladá Boleslav into the Jizera River at concentrations ranging from ng/L to μg/L. Acesulfame and oxypurinol in concentrations exceeding 100 ng/L systematically occurred, and then a few tens of ng/L of carbamazepine, sulfamethoxazole, primidone, and lamotrigine were regularly detected at the water outlet using the artificial recharge for production of drinking water. Bank infiltration was found more efficient in removing PPCP substances at the Káraný locality where none of the monitored substances was systematically detected in the mixed sample.