Chronic disease burdens continue to rise in highly dense urban environments where clustering of type II diabetes mellitus, acute myocardial infarction, stroke, or any combination of these three conditions is occurring. Many individuals suffering from these conditions will require longer-term care and access to clinics which specialize in managing their illness. With Singapore as a case study, we utilized census data in an agent-modeling approach at an individual level to estimate prevalence in 2020 and found high-risk clusters with >14,000 type II diabetes mellitus cases and 2000–2500 estimated stroke cases. For comorbidities, 10% of those with type II diabetes mellitus had a past acute myocardial infarction episode, while 6% had a past stroke. The western region of Singapore had the highest number of high-risk individuals at 173,000 with at least one chronic condition, followed by the east at 169,000 and the north with the least at 137,000. Such estimates can assist in healthcare resource planning, which requires these spatial distributions for evidence-based policymaking and to investigate why such heterogeneities exist. The methodologies presented can be utilized within any urban setting where census data exists.