A range of methods are available for assessing ecosystem services. Methods differ in their aims; from mapping and modelling the supply and demand of ecosystem services to appraising their economic and non-economic importance through valuation techniques. Comprehensive guidance for the selection of appropriate ecosystem service assessment methods that address the requirements of different decision-making contexts is lacking. This paper tackles this gap using the experience from 27 case studies which applied different biophysical, socio-cultural and monetary valuation methods to operationalise the ecosystem service concept towards sustainable land, water and urban management. A survey of the reasons why the case study teams selected particular methods revealed that stakeholder-oriented reasons, such as stakeholder participation, inclusion of local knowledge and ease of communication, and decision-oriented reasons, such as the purpose of the case study and the ecosystem services at stake, were key considerations in selecting a method. Pragmatic reasons such as available data, resources and expertise were also important factors. This information was used to develop a set of linked decision trees, which aim to provide guidance to researchers and practitioners in choosing ecosystem service assessment methods that are suitable for their context.