Finland and Poland share similar environmental interests with regard to their wastewater effluents eventually being discharged to the Baltic Sea. However, differences in the influent wastewater characteristics, treatment processes, operational conditions, and carbon intensities of energy mixes in both countries make these two countries interesting for carbon footprint (CF) comparison. This study aimed at proposing a functional unit (FU) which enables a comprehensive comparison of wastewater treatment plants (WWTPs) in terms of their CF. Direct emissions had the highest contribution (70%) to the total CF. Energy consumption dominated the total indirect emissions in both countries by over 30%. Polish WWTPs benefitted more from energy self-sufficiency than Finnish plants as a result of higher electricity emission factors in Poland. The main difference between indirect emissions of both countries were attributed to higher chemical consumption of the Finnish WWTPs. Total pollution equivalent removed (TPErem) FU proposed enabled a better comparison of WWTPs located in different countries in terms of their total CF. High correlations of TPErem with other FUs were found since TPErem could balance out the differences in the removal efficiencies of various pollutants. Offsetting CF was found a proper strategy for the studied WWTPs to move towards low-carbon operation. The studied WWTPs could reduce their CF from up to 27% by different practices, such as selling biofuel, electricity and fertilizers. These findings are applicable widely since the selected WWTPs represent the typical treatment solutions in Poland, Finland and in the Baltic Sea region.