This paper aims to understand how a group of academics cite each others’ work through time, considering the simultaneous co-evolution of three networks representing their scientific collaboration, the journals in which they publish and institutional membership. It argues that both social and cognitive processes contribute to these dynamics. Two types of network mechanisms are considered specifically: closures by affiliation and closures by association. To assess whether these mechanisms generate the macro features of the network under study, we propose new features for three-mode multilevel networks such as the mixed geodesic distances, mixed degree distributions, and the mixed quadrilateral census. We investigate whether a micro-level model that considers the above-mentioned network mechanisms is able to correctly reproduce these features. We apply stochastic actor-oriented models (SAOMs) for one-mode and two-mode networks to link the micro-macro processes using a dataset of a scientific community of astronomers from 2013 to 2015. The results suggest that social relationships grounded on scientific collaboration and proximity based on institutional affiliation are more accurately suited to understanding the co-evolution of the network of citations than an alternative approach that merely considers cognitive-based networks measured as the similarity in publishing in the same journals.