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Background Diarrhoea remains the major cause of morbidity and mortality of children under five years in Africa. Several studies have shown that inadequate and unsafe water, lack of sanitation, and poor hygiene practices are complex issues for different pathogens and accountable for the occurrence of diarrhoea diseases. We assessed the combined effect of household’s source of drinking water and type of toilet facility and residential wellbeing on the incidence of childhood diarrhoea in 33 Sub-Saharan Africa countries while accounting for relevant compositional and contextual factors. Methods The 2010–2019 datasets from the Demographic and Health Surveys were drawn for analyses. The outcome variable used in this study was the incidence of childhood diarrhoea. Three negative log-log generalized linear regression models were then sequentially fitted to the data to examine the joint effect of household water and sanitation practices on child diarrhoea. The results were presented using crude odds ratios (CORs) and adjusted odds ratios (AORs) at 95% confidence intervals (CIs). Using ArcGIS software, maps were design to unveil the spatial distribution of key variables. Findings Approximately 16% of the 307,741 mothers interviewed reported an incidence of diarrhoea disease among children under-five years in their households. The results showed that a household depending on an unimproved source of drinking water and with an unimproved type of toilet facility was not significantly associated with childhood diarrhoea. However, those with improved drinking water but an unimproved type of toilet facility had higher odds of reporting childhood diarrhoea (AOR = 1.020, 95% CI = 1.003-1-036) compared to those in households with both improved source of drinking water and type of toilet facility. Across the geographical regions, Eastern (aOR = 1.102, 95% CI = 1.084–1.120) and Central Africa (aOR = 1.102, 95% CI = 1.083–1.121) were more likely to experience child diarrhoea. Conclusion Water and sanitation practices such as the source of drinking water and toilet facility, and geographic region had significant effects on childhood diarrhoea in sub-Saharan Africax. The findings suggest the need for multi-sectoral actions that recognise the geo-spatial and temporal characteristics identified in the study through regional to national policies. Water and sanitation community-based interventions that seek to improve equitable access to safe water and sanitation in the sub-region should be intensified.

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