The general aim of the present chapter is to focus on the factors influencing simulation-based computersupported inquiry learning in small groups. The authors will give an overview of research that describes different factors influencing inquiry learning and problem solving and will add a dimension of collaborative web-based inquiry from their studies. The evidence from relevant scientific literature as well as the empirical results collected by the authors form the basis for discussion about designing an effective learning environment through a viewpoint of different end-users of our results – especially teachers and software designers. As a result, three additional main factors have been found that should be taken into account in designing support systems for problem solving: i) the level of difficulty of problems, ii) the appropriate sequence of problems, and iii) the characteristics of learners’ groups.