Historic increase in urban population numbers in the face of shrinking urban economies and declining social services has meant that a large proportion of the urban population lives in precarious urban conditions, which provide the grounds for high urban health risks in low income countries. This study aims to identify, investigate, and contrast the spatial patterns of vulnerability and risk of two major causes of mortality, viz malaria and diarrhea mortalities, in order to optimize resource allocation for effective urban environmental management and improvement in urban health. A spatial cluster analysis of the observed urban malaria and diarrhea mortalities for the whole city of Accra was conducted. We obtained routinely reported mortality data for the period 1998–2002 from the Ghana Vital Registration System (VRS), computed the fraction of deaths due to malaria and diarrhea at the census cluster level, and analyzed and visualized the data with Geographic Information System (GIS, ArcMap 9.3.1). Regions of identified hotspots, cold spots, and excess mortalities were observed to be associated with some socioeconomic and neighborhood urban environmental conditions, suggesting uneven distribution of risk factors for both urban malaria and diarrhea in areas of rapid urban transformation. Case–control and/or longitudinal studies seeking to understand the individual level factors which mediate socioenvironmental conditions in explaining the observed excess urban mortalities and to establish the full range of risk factors might benefit from initial vulnerability mapping and excess risk analysis using geostatistical approaches. This is key to evidence-based urban health policy reforms in rapidly urbanizing areas in low income economies.