In order to develop potentially transformative Web 2.0 tools in higher education, the complexity of existing academic practices, including current patterns of technology use, must be recognised. This paper describes how a series of participatory design activities allowed postgraduate students in education, social sciences and computer sciences to contribute to the development of new Web 2.0 tools to enhance an existing virtual collaboration environment. In the course of these design activities, students reflected on and articulated the existing and emerging academic practices in which they were involved as they managed their transition from undergraduate courses to postgraduate research. The tools that were developed can therefore be seen as reifications of participants' emerging academic practices and the challenges they face as new researchers. This highlights the need for flexible design approaches and adaptable technological frameworks if Web 2.0 tools are to be successfully integrated into higher education settings. (Contains 4 figures.)