The dataset contemplates the concentration of micropollutants in irrigation waters coming as effluents from 2 setups of a pilot-scale wastewater treatment plant (RW-1 & RW-2) of a wastewater treatment plant at pilot scale in Lesvos, Greece. Samples were collected along 5 campaigns (C0-C4), which comprise different periods of crops growth. The concentration (in ng/L) of 65 micropollutants in the water samples is depicted on both tables, along with the analytical parameters as method detection and quantification limits and recovery.