Self-regulated learning (SRL) with hypermedia environments involves a complex cycle of temporally unfolding cognitive and metacognitive processes that impact students' learning. We present several methodological issues related to treating SRL as an event and strengths and challenges of using online trace methodologies to detect, trace, model, and foster students' SRL processes. We first describe a scenario illustrating the complex nature of SRL processes during learning with hypermedia. We provide our theoretically driven assumptions regarding the use of several cognitive methodologies, including concurrent think aloud protocols, and provide several examples of empirical evidence regarding the advantages of treating SRL as an event. Last, we discuss challenges for measuring cognitive and metacognitive processes in the context of MetaTutor, an intelligent adaptive hypermedia learning environment. This discussion includes the roles of pedagogical agents in goal-generation, multiple representations, agent-learner dialogue, and a system's ability to detect, track, and model SRL processes during learning. (Contains 3 footnotes, 3 tables, and 3 figures.)