There are many challenges associated with Inquiry-Based Practical Work (IBPW), scattered in the school and post-school natural sciences education research literature. The goal of the systematic review presented in this paper, was to gather the contextual teaching challenges in the said literature, and then to create a detailed multi-perspective description of these challenges. The result shows that, the challenges occur mostly in the northern hemisphere, the highest proportion is in the Upper- and Post-secondary education levels, and more than half of the challenges are in integrated natural sciences education settings. In addition, the challenges are deeply divided between the school- and system-levels of the education framework, with the emergence of seven categories that have not been reported before. While significantly increasing knowledge, the results can be used when supporting teachers implementing IBPW. This is in addition to informing future research, around teacher support and the further unravelling of the challenges.