The COVID-19 pandemic has been particularly threatening to the patients with end-stage kidney disease (ESKD) on intermittent hemodialysis and their care providers . Hemodialysis patients who receive life-sustaining medical therapy in healthcare settings, face unique challenges as they need to be at a dialysis unit three or more times a week, where they are confined to specific settings and tended to by dialysis nurses and staff with physical interaction and in close proximity . Despite the importance and critical situation of the dialysis units, modelling studies of the SARS-CoV-2 spread in these settings are very limited . In this paper, we have used a combination of discrete event and agent-based simulation models, to study the operations of a typical large dialysis unit and generate contact matrices to examine outbreak scenarios . We present the details of the contact matrix generation process and demonstrate how the simulation calculates a micro-scale contact matrix comprising the number and duration of contacts at a micro-scale time step . We have used the contacts matrix in an agent-based model to predict disease transmission under different scenarios . The results show that micro-simulation can be used to estimate contact matrices, which can be used effectively for disease modelling in dialysis and similar settings.