Web‐based learning is becoming prevalent in science learning. Some use specially designed programs, while others use materials available on the Internet. This qualitative case study examined the process of acquisition of integrated science process skills, particularly the skill of controlling variables, in a web‐based learning environment among grade 5 children. Data were gathered primarily from children’s conversations and teacher–student conversations. Analysis of the data revealed that the children acquired the skill in three phases: from the phase of recognition to the phase of familiarization and finally to the phase of automation. Nevertheless, the acquisition of the skill only involved the acquisition of certain subskills of the skill of controlling variables. This progression could be influenced by the web‐based instructional material that provided declarative knowledge, concrete visualization and opportunities for practise.