The present paper describes a series of case studies of collaborative learning supported by two web-based learning environments: Synergeia2 and FLE3. The case studies were conducted in Finland, Greece, Italy, and the Netherlands as a part of international project called Innovative Technologies for Collaborative Learning. The general aim of this investigation was to examine the cases in a detailed way, and to find possible indications that might explain success and difficulties related to implementation of web-based Collaborative Learning Environments. The specific aims of the present study were to investigate the nature of the students' and teachers' computer-mediated discourse, whether and to what extent the students and teachers actually used the knowledge types in Synergeia2 and FLE3-environments (resembling CSILE's thinking types); and finally, to what extent the use of knowledge types was connected to the content of knowledge produced by the students and the teachers. The results showed considerable differences in the nature of the discourse and difficulties in students' labelling of their own notes. It is suggested that the adoption and development of collaborative practices takes time: collaborative learning in web-based environments is best organized around long-lasting learning activities; instead of weeks, whole academic terms. Further, it is underlined that the selection of good sets of knowledge types is important. Software must allow teachers to construct appropriate sets of knowledge types.