Water pollution by contaminants of emerging concern (CECs) causes risks to both the environment and human health. We assessed water pollution by CECs in the Sava River basin in two monitoring campaigns carried out in May and July 2017. The grey water footprint (GWF) is a tool that converts the level of pollution by particular substances into the volume of water needed for dilution to a harmless level. Therefore, it can serve as an indicator for comparing various pollutants. The results show that substances that determine the GWF differ in individual locations. The highest value of the GWF was associated with 17β-estradiol, however, found only in one wastewater sample. The study showed that the value of the GWF in individual locations fluctuates and does not depend on the size of the wastewater treatment plant from which the wastewater is discharged. At selected wastewater treatment plants, a sustainability assessment was carried out using the Water Pollution Level indicator. The values in all cases were below the level of 1.0, indicating sustainable discharge; only in two cases did values reach the defined threshold to question the potential of non-sustainable discharge. The study contributes to earlier studies on the GWF and enlarges knowledge regarding the GWF of CECs.