The boom in Internet and communication technology has accelerated change in information delivery channels from paper to networked, digital displaying devices. Reading electronically has altered the cognitive and metacognitive processes readers use to approach science texts. Assessing reading in a digitized environment also opens up opportunities to examine the recursive process of self-regulated learning. However, a systematic analysis in this area across paper- and e-based environments is lacking. This study explores methods of assessing metacognition in reading informational science texts to address this gap. A total of 55 studies in 47 articles published from 1990 to 2016 investigating effects of metacognition on science reading are reviewed. The analysis reveals frequently applied methods, including self-report questionnaires for measuring metacognitive knowledge, event-based assessment for metacognitive skills, and questionnaires or interviews for metacognitive experiences. Community acceptable instruments are presented and illustrated. E-based environment has potential to support comprehensive and complicated measurement of metacognition. Future research may further the investigation of interactions among metacognitive components by designing sequential tasks and combining multiple assessment methods. Finally, triangulation of findings from various methods is essential in assessing metacognition involved in self-regulated reading.