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Transdisciplinary research (TR) develops descriptive, normative and practice-oriented knowledge in order to help solve, mitigate or prevent life-world problems. TR deals with problem fields in such a way that it can (a) grasp the complexity of problems, (b) take into account the diversity of scientific and life-world perceptions of problems, (c) link abstract and case-specific knowledge, and (d) develop knowledge and practices that promote what is perceived to be the common good. For these purposes disciplinary researchers and actors of the life-world collaborate. They contribute substantial knowledge about the issue (practical experience, scientific models, results) as well as formal approaches (methods from systems dynamics, operational or action research, etc.). These knowledge bases have to be interrelated and transformed through the specific problem field during the research process: in problem identification and structuring, in problem analysis as well as in bringing results to fruition. We discuss the interrelation of knowledge bases in relation to requirements a-d. Furthermore, we identify particular transdisciplinary challenges and propose methods and tools to address them.