This is an interpretive case study seeking to develop detailed and comparative descriptions of how two groups of fifth-grade students used two different Computer-based Programming Environments (CPEs) (namely Microworlds Logo and Stagecast Creator) during scientific modelling. The primary sources of data that were used in this 4-month study include videotaped students' group work and whole-class discussions, and the instructors' reflective journals. For the data analysis, contextual inquiry was used in conjunction with analysis of student conversation in order to gain better insight into students' activity and conversation patterns while working with CPEs. Findings highlight the differences in the ways that the students used the two CPEs in the context of developing models of natural phenomena with respect to three distinct phases that emerged from data analysis, which include student approaches to (i) planning, (ii) writing and debugging code, and (iii) using code to represent the phenomenon under study. Lastly, findings highlight which aspects of students work during the three phases can be productive for scientific modelling, proposing possible relationships between student work and CPE features. (Contains 3 tables, 10 figures and 1 note.)