Drinking water treatment systems (DWTSs) are energy intensive facilities, and are an example of the water-energy nexus. Benchmarking energy efficiency is a valuable tool for improving the economic and environmental performance of such facilities. Data envelopment analysis (DEA) is typically used to assess efficiency, allocating flexible weights (FSW) to variables that maximise energy efficiency scores for each DWTS (DEA-FSW). It means that different conditions are applied to each DWTS. Moreover, the DEA-FSW approach has finite discriminatory power which limits cross-unit comparison of energy efficiency hindering the benchmarking of DWTSs. To overcome these limitations, our study explored the effect of estimating the energy efficiency scores of DWTSs by allocating common sets of weights (CSW) within DEA (DEA-CSW). This approach was applied empirically on a sample of 146 DWTSs. Evaluated DWTSs had poor energetic performance based on both DEA-FSW and DEA-CSW estimates (low energy efficiency scores: 0.329 and 0.163, respectively). Even in the optimistic scenario, the average energy efficiency score was low (0.220), with potential electricity savings of 78 % by DWTPs when energy efficient. Unlike DEA-FSW, DEA-CSW allowed energy efficient DWTSs to be distinguished from the 146 facilities. Significant differences in the weights allocated to electricity and pollutants removed from raw water were reported for both approaches, and contributed to diverging energy efficiency scores. In conclusion, this study demonstrated the relevance of using suitable methods to generate comparable results for water companies, allowing the energy performance of DWTSs to be objectively evaluated for benchmarking purposes.