The conventional means of imparting knowledge in higher education institutions have considerably changed throughout time with the innovations of Information and Communication Technologies (ICTs). Courses disseminated are either fully online or on a blended learning mode. While the growth rate of online learning is higher compared to the traditional mode, we also find that online learners lack the pedagogical support to help them pursue successfully their studies online. With a growing feeling of isolation due to lack of interaction online, they end up withdrawing from the course. Whereby the necessity to develop an online learning environment to meet the pedagogical needs of students. In support to higher education institutions, learning management systems (LMS) provide the core learning platforms for an online environment. However to assess how effective an online learning environment is, universities need to measure how well these LMS deliver their key functions and fulfill the pedagogical needs of learners online. This paper explores initially the perceptions of learners following the use of Moodle as well as the barriers they face. This exploratory study was conducted through a web survey to learners engaged in blended learning. Once the data was collected and analyzed, with the use of the Community of Inquiry Framework, which is considered as the model which provides insights to the dimensions of an effective online learning environment, we explored how effective the main functionalities and tools available on Moodle provided the pedagogical supports students needed online. Overall results show that students use Moodle to access notes rather than as an online learning environment where interaction between peers and instructor should have been done. The mapping results show that modules are present on Moodle to support learners in their studies. However the functionalities and tools need to be used fully to be beneficial.