The Mekong Delta is the most vulnerable region to extreme climate and hydrological conditions however the association between these conditions and children?s health has been little studied. We examine the association between annual river flood pulse and paediatric hospital admissions in a Vietnam Mekong Delta city. Daily paediatric hospital admissions (PHA) were collected from the City Paediatric Hospital, and daily river water level (RWL) and meteorological data were retrieved from the Southern Regional Hydro-Meteorological Centre from 2008 to 2011. We evaluated the association between annual river flood pulse (>=90th percentile of RWL) and PHA using the Poisson distributed lag model, controlling for temperature, relative humidity, day of week, seasonal and long-term trends. The seasonal pattern of PHA was examined using harmonic and polynomial regression models. The cumulative risk ratios estimated for a 15-day period following an extreme RWL was 1.26 (95%CI, 1.2-1.38) for all age groups, 1.27 (95%CI, 1.23-1.30) for under five-years and 1.15 (95%CI, 1.07-1.20) for school-aged children, 1.24 (95%CI, 1.21-1.27) for all-causes, 1.18 (95%CI, 1.12-1.21) for communicable infection, 1.66 (95%CI, 1.57-1.74) for respiratory infection and 1.06 (95%CI, 1.01-1.1) for other diseases. The peak PHA risk is in the September-October period corresponding to the highest RWL, and the PHA-RWL association was modified by temperature. An increase in PHA is significantly associated with annual river flood, and the pattern of PHA is seasonally correspondent to the RWL. These findings combined with projected changes in climate conditions suggest important implications of climate change for human health in the Mekong Delta region.