Little is known about the impacts of morphological indicators that can be derived from the physical environment on the risk of diarrhoeal diseases. Given Africa’s recent explosive urbanisation rates and rapid changes in landscape, coupled with a high burden inflicted by diarrhoeal diseases, urban planners and public health officials in that region can benefit from a deeper understanding of the relation between urban morphology and diarrhoeal diseases. This work presents a large-scale ecological analysis based on open-access data to readily identify risk factors related to diarrhoeal diseases originating from the physical environment. Designed as a proof-of-concept study, this work is a cross-sectional analysis that focuses on Ivorian urban centres. Differently from previous spatial epidemiology studies on diarrhoea, we advance a set of morphological indicators based on landscape metrics and infrastructures as key variables of exposure, exploring their relationship with prevalence and mortality rates attributed to diarrhoea. This ecological analysis aims simultaneously to (i) build an analytical framework based strictly on free, open-access data and open-source software to investigate diarrhoea risk factors originating from the physical environment; and (ii) understand whether different urban patterns, defined by land-use and distribution of basic infrastructures, are related to different prevalence rates of diarrhoeal diseases.