As online postsecondary educational offerings become more common in response to situations such as the COVID pandemic and increased calls for education that is accessible remotely, the question of how problem-based learning (PBL) can be adapted to the distance environment is being more closely considered. The purpose of this mixed methods study was to use the cognitive presence indicators of the Community of Inquiry (CoI) framework to compare the online discussion activity of distance and blended (face-to-face combined with online) undergraduate environmental science students engaged in online PBL. This framework describes cognitive presence using four indicators: triggering events, exploration, integration, and resolution. Data consisted of compiled archived asynchronous discussion posts by 108 distance and 144 blended Bachelor of Science in Environmental Science students from Royal Roads University engaged in an asynchronous online PBL exercise. Frequency counts for each indicator were used for quantitative comparisons while qualitative data were examined using content analysis and thread mapping. The content analysis involved categorizing posts using the cognitive presence indicators. Thread maps showed the organization and timing of the discussion with the cognitive indicator coding highlighted. The CoI framework was expanded upon with the addition of organization as a new cognitive indicator. This indicator contributed to the identification of two major discussion approaches in the thread maps: organic discussions and structured discussions. It also helped to capture the peer-to-peer teaching that is necessary for the organization of the discussion and support for the group’s cognitive presence.