The literature on scientific modelling practices in science education has provided a fruitful discussion on how learners tend to view models vs. how and what they should think about them. One approach is to teach students that models are abstractions so that they do not view them as a copy of phenomena they represent. Although teaching students that models are abstractions is a successful strategy in modelling instruction, we still do not know how students engage in and work towards the process of abstraction while they develop a model to understand scientific ideas. This qualitative study examines how a group of undergraduate and graduate students in an upper-level ecosystem ecology course at a research university in the southeastern part of the United States engage in a task that requires constructing an abstract representation of how biogeochemical cycles work by using a specific approach to modelling, namely synthesis modelling. Data corpus entailed paired interviews with ten students and their artefacts. The findings centred upon four episodes regarding how students engage in abstraction through a synthesis approach to modelling as they make sense of the system of biogeochemical cycles: working with surface similarities, abstracting ideas, abstracting structures, and checking on model-source fit.