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In science education, a significant portion of the research effort is devoted to the identification of the tools, activities and/or methods that could support students’ conceptual understanding and facilitate their engagement in inquiry processes. This paper presents different aspects of the use of web-based tools in the teaching of the basic science concepts which are involved in an environmental phenomenon (greenhouse effect) via inquiry-based processes. Initially, a specific web-based tool (Web-based Inquiry Science Environment, WISE) is analyzed in order to bring out the inquiry processes that students are engaged in when it is applied in the science classroom. Subsequently, a qualitative analysis is being conducted with regard to the views of Greek secondary school teachers’ on how a tool of this type may be integrated in science classes focusing on advancement of science learning in a way that coherence between scientific practices and content is maintained.