This study investigates how cohesion manifests in readers’ thought processes while reading texts when they are instructed to engage in self-explanation, a strategy associated with deeper, more successful comprehension. In Study 1, college students (n = 21) were instructed to either paraphrase or self-explain science texts. Paraphrasing was characterized by greater cohesion in terms of lexical overlap whereas self-explanation included greater lexical diversity and more connectives to specify relations between ideas. In Study 2, adolescent students (n = 84) were provided with instruction and practice in self-explanation and reading strategies across 8 sessions. Self-explanations increased in lexical diversity but became more causally and semantically cohesive over time. Together, these results suggest that cohesive features expressed in think alouds are indicative of the depth of students’ comprehension processes.