The ecosystem service (ES) concept has increasingly been applied in environmental planning, while there are several decades of experience in applying multi-criteria decision analysis (MCDA) in complex planning situations. The aim of this article is to assess how the ES concept has been used in water management projects together with MCDA and to examine the experiences gained and make recommendations to overcome any identified challenges. Our conclusions are based on a systematic analysis of 23 articles that were selected among 206 articles focused on water-related studies using, for example, the terms multi-criteria and ecosystem services in the title, abstract or keywords. Here, we explore (i) at what level of detail ESs are included in the decision hierarchy, (ii) the pros and cons of the complementary use of the two approaches, and (iii) how the potential challenges related to the use of MCDA, such as the large number of criteria, double-counting, or assigning criteria weights, are addressed in the selected cases. The results reveal large differences between the case studies. It is shown that only a few case studies used ES categories to classify criteria in the decision hierarchy, that these cases included different numbers of ES criteria and non-ES criteria, and that most case studies elicited stakeholder preferences in MCDA. Although the paper focuses on water management projects, the conclusions regarding the advantages and pitfalls of the complementary use of the methods, as well as our recommendations, are also applicable to other environmental management contexts.