Behavioural and environmental heterogeneities among host populations can play an important role in hantavirus transmission. We designed an agent-based model to determine the relative role of direct and indirect transmission on Sin Nombre hantavirus (SNV) dynamics in deer mice, incorporating host heterogeneities. We parameterized the model to reproduce aggressive encounters, movement and excretions from field-based studies and lab experiments. Our model captured known properties of SNV spread and matched the outcomes of transmission experiments. Although the model was not fit to R0 values, the R0 distribution from our simulations was similar to values from other hantavirus models. We also found that a small per cent of mice were responsible for a high per cent of direct transmission. Our model indicated that mouse heterogeneity and environmental contamination are both important. Model extensions can explore larger ecosystem dynamics by incorporating temporal heterogeneity, to understand how changes in host characteristics and environment influence SNV transmission.