In the present study, we first examined the formality and use of academic language in students' scientific explanations in the form of written claim, written evidence, and written reasoning (CER). Middle school students constructed explanations within an intelligent tutoring system after completing a virtual science inquiry investigation. Results showed that students tended to use more formal, academic language when constructing their evidence and reasoning statements. Further analyses showed that both the number of words and pronouns used by students were significant predictors for the quality of students' written claim, evidence, and reasoning statements. The quality of claim statements was significantly reduced by the lexical density (type-token ratio) of student writing, but quality of reasoning significantly increased with lexical density. The quality of evidence statements increased significantly with the inclusion of causal and temporal relationships, verb overlap as captured by latent semantic analysis, and inclusion of descriptive writing. These findings indicate that students used language differently when constructing their claim, evidence, and reasoning statements. Implications for instruction and scaffolding within intelligent tutoring systems are discussed in terms of how to increase students' knowledge of and use of academic language.