An inquiry-based learning pedagogy coupled with a seamless learning environment is a potential way to realise the educational goal of learner-centred learning in digital classrooms in the 21st century. An overarching research framework is proposed for preparing teachers to effectively develop pedagogical designs that are premised on theoretical principles and facilitate inquiry-based learning in a seamless learning environment. We carried out an initial study using the overarching framework. Three questions are addressed: how a principle-based pedagogical design was developed and implemented, the effect that the principle-based pedagogical design had on students' domain knowledge gains and inquiry skills and how students advanced their domain knowledge and developed their inquiry skills. One teacher and 27 students from a local primary school were involved in the study. Both qualitative and quantitative data were collected and analysed over two weeks. Six inquiry-based learning lessons focusing on a scientific "rustproofing" learning unit were conducted in a seamless learning environment, initiated in a digital classroom and extended to online discussions on a social network platform. The results reveal innovative ways of developing and implementing the pedagogical design in the rustproofing learning unit and demonstrate the pedagogical design's positive effect on students' domain knowledge gains and inquiry skills. In addition, how the students advanced their domain knowledge and inquiry skills were also explored and discussed.