The purpose of this study is to discuss major issues in designing inquiries on the web. Instructional designers face a lot of difficulties and challenges to deal with in the course of designing inquiry experiences for learners in the online environment, a complex and ill-structured learning environment. Facilitating inquiry or using an inquiry-based learning approach on the web has both advantages and disadvantages. Instructional designers need to acknowledge the design issues arising in each and every phase of the design process. Utilising appropriate design strategies, instructional designers can provide positive learning experiences for their online learners. For this purpose, three representative cases in the context of teacher professional development were examined and six major issues were identified as follows: (1) seeking a balance between a system-generated guide and human facilitator, (2) visual representation of the inquiry process, (3) motivating learners with the right question, (4) engaging learners in various learning activities, (5) guiding the inquiry process with various scaffolds, and (6) maximising learning by coordinating resources, tools and the community of inquiry. This study explains each issue in great detail and provides possible guides for instructional designers to handle the issue.