The aim of this explorative study was to find the factors limiting sixth-grade learners' outcomes in acquiring skills related to the transformative inquiry learning processes as well as to analyse the interrelations between inquiry skills in order to develop an optimal support system for designing Web-based inquiry learning environments. A Web-based learning environment "Young Scientist" was developed and applied to the domain of integrated science. The skill of identifying the correct research questions appeared to be a prerequisite for formulating research questions. When students understand how to identify the research questions correctly, there is no need for supporting formulation of research questions or hypotheses. We have found that at the stages of analysing data and inferring, students have to be provided with the tools to activate their prior knowledge, assignments help to organize their work into manageable sections, and reflective support or adaptive feedback to relate the results achieved with the process of inquiry. Our findings demonstrate that the effectiveness of inquiry learning can be strongly influenced by regulative support; however, a particular level of initial inquiry knowledge in theoretical context is also needed in order to develop inquiry skills in a situational context.