Analyzing costs and greenhouse gas (GHG) emissions could be of great importance for the water utilities to supply water services in a healthy and sustainable manner. In this study, we measured the eco-efficiency of several water utilities in England and Wales by incorporating GHG as an undesirable output. For the first time, we evaluated the eco-efficiency of the water production process using robust cross-efficiency data envelopment analysis (DEA) techniques. The further use of clustering and regression techniques allowed us to better understand the drivers of eco-efficiency. The results showed that the mean eco-efficiency of the water sector was 0.748, which indicates that costs and GHG emissions could be reduced by 25.2% to generate the same level of output. Large water companies with high energy costs and levels of GHG emissions belonged to the less eco-efficient group. Environmental factors related to density, topography, and treatment complexity further impacted eco-efficiency. Finally, we linked our results to the regulatory cycle and discuss some policy implications.