This paper focuses on the use of Life Cycle Assessment (LCA) to evaluate the performance of seventeen control strategies in wastewater treatment plants (WWTPs). It tackles the importance of using site-specific factors for nutrient enrichment when decision-makers have to select best operating strategies. Therefore, the LCA evaluation is repeated for three different scenarios depending on the limitation of nitrogen (N), phosphorus (P), or both, when evaluating the nutrient enrichment impact in water bodies. The LCA results indicate that for treated effluent discharged into N-deficient aquatic systems (e.g. open coastal areas) the most eco-friendly strategies differ from the ones dealing with discharging into P-deficient (e.g. lakes and rivers) and N&P-deficient systems (e.g. coastal zones). More particularly, the results suggest that strategies that promote increased nutrient removal and/or energy savings present an environmental benefit for N&P and P-deficient systems. This is not the case when addressing N-deficient systems for which the use of chemicals (even for improving N removal efficiencies) is not always beneficial for the environment. A sensitivity analysis on using weighting of the impact categories is conducted to assess how value choices (policy decisions) may affect the management of WWTPs. For the scenarios with only N-limitation, the LCA-based ranking of the control strategies is sensitive to the choice of weighting factors, whereas this is not the case for N&P or P-deficient aquatic systems.