This population-based epidemiologic study investigated the associations of individuals' socio-demographic statuses, sanitary systems and habits, water supply and drainage conditions with diarrhoea incidences among 707 children younger than 5 years who were living in slum communities with various water logging patterns in Dhaka, Bangladesh. We conducted a home-visiting survey during the pre-monsoon period from December 2006 to April 2007. Nine slum communities were selected that had been experiencing five different water logging conditions. One non-water logging community was selected as a control. The Disability Adjusted Life Years (DALYs) were calculated using data on diarrhoea morbidity and mortality. Although DALYs lost because of diarrhoea were very small in a non-inundation type community, but were the highest in persistent drainage inundation type communities. Among the factors correlated with DALYs, control variables for mother's illiteracy and household income strongly attenuated most of these correlations to statistical null, except for mother's age (less than 15 years-old), using hanging latrine and not washing hands before eating, and after defecation. In conclusion, water logging conditions and socio-economic statuses may strongly contribute to diarrhoea incidence in the city's slum communities. In such communities, interventions to address both water logging and socio-economic conditions may be critical for reducing diarrhoea incidences.