Chapter 3 aims to guide the reflexive social-ecological systems (SES) researcher through different components of an SES research project. The chapter focuses on the identification of research problems, the purpose of the research and the SES research areas within which a researcher may be embedded. It also elaborates on more general issues relating to data generation, participatory research along a gradient of collaboration, as well as computational and mathematical modelling approaches, as these are common to a number of specific methods discussed in Part 2 of the book. Finally, practical ethical considerations associated with SES research are considered.