Computer-supported collaborative inquiry learning (CSCiL) has been proposed as a successful learning method to foster scientific literacy. This research aims to bridge the knowledge gap surrounding the role of peers as scaffolding sources in CSCiL environments. The primary objective is to explicitly implement peer assessment as a scaffolding tool to enhance students' inquiry output in terms of research question, data, and conclusion. Additionally, students' perceptions of peer assessment within CSCiL are explored. The study involved 9th and 10th-grade students from 12 schools (N = 382), exploring the effects of peer assessment with and without peer dialogue. The results highlight that while adjustments were more frequently made to the research question and data, adjustments to the conclusion showed significantly greater improvement. Furthermore, students' perceptions of peer assessment during CSCiL were examined, revealing that students generally perceive peer assessment as fair and useful, and they accept it while being willing to make improvements based on the feedback. While students did not report experiencing negative feelings, they also did not report positive emotions from the process. Additionally, the study found that including a peer dialogue in the peer assessment process did not significantly impact the abovementioned findings. This study enriches our understanding of peer assessment as a scaffolding tool in CSCiL, highlighting its potential to improve inquiry outputs and providing valuable insights for instructional design and implementation.