Integrated assessment is rapidly developing in the scientific as well as policy community. Different methods, techniques and procedures (i.e., tools) are used in these assessments. Often, the choice for using certain tools in an assessment is not well founded. This paper presents a framework that scientifically underpins the role of, and thus choice for, tools within an integrated assessment. The ... [Show full abstract] framework identifies four phases in an integrated assessment, which are derived from the complementarities between various forms of integrated assessments. Tasks have to be done within each of the four phases. Seven types of tools with similar characteristics are matched to those tasks. The tool framework is a theoretical construct, developed whilst keeping in mind perceptions and suggestions from eventual users. It is a first step in the development of an overarching framework for finding appropriate tools for different tasks in an assessment, and justifying the use of those tools.