Flow theory identifies several structural variables that can be manipulated by an instructional designer. Modifying these variables may cause an increase in the likelihood that a learner will be motivated to continue with the lesson. While some researchers suggest activity contents, such as challenge and goal and induce flow experience [1], others hypothesize flow is enhanced by vividness and interactivity of the presentation [2]. This study investigates the effect of activity content, its presentation, and the interactions between the two on flow experience (intrinsic motivation) in instructional activity. The results suggested that the activity content has major influences on motivation, but presentation is a double-edge sword. Hypermedia presentation adds appeals to instructions that motivate students if they are used appropriately. When the content relevance is complicated, complex presentations can be distracting. Consequently, hypermedia elements should be used sparingly at the beginning of a lesson when challenges are high and students are unfamiliar with the material. As the lesson progresses it could be used gradually as the content challenges are reduced.