Improving the environmental performance and energy efficiency of cooling towers requires systematic evaluation. However, methodological challenges emerge when applying typical environmental assessment methods to cooling towers. Hence, this paper compares the methods, analyzes their strengths and weaknesses, and proposes adaptions for evaluating cooling towers. As a case study, we applied five methods for assessing the wet cooling system of the high‐performance data center in Stuttgart. These are material flow analysis (MFA), life cycle inventory, life cycle assessment (LCA), exergy analysis, and life cycle exergy analysis (LCEA). The comparison highlights that the LCA provides the most comprehensive environmental evaluation of cooling systems by considering several environmental impact dimensions. In the case of the wet cooling tower, however, electricity and water consumption cause more than 97% of the environmental impacts in all considered impact categories. Therefore, MFA containing energy flows suffices in many cases. Using exergy efficiency is controversially debated because exergy destruction is part of the technical principle applied in cooling towers and, therefore, difficult to interpret. The LCEA appears inappropriate because construction and disposal barely affect the exergy balance and are associated with transiting exergy. The method comparison demonstrates the need for further methodological development, such as dynamic extensions or the efficiency definition of cooling towers. The paper highlights that the methodological needs depend on the specific application.