There is limited knowledge on the effect of seasonal flooding on health over time. We quantified the short- and long-term effects of floods on selected health indicators at public healthcare facilities in 11 districts in Cambodia, a flood-prone setting. Counts of inpatient discharge diagnoses and outpatient consultations for diarrhea, acute respiratory infections, skin infections, injuries, noncommunicable diseases and vector-borne diseases were retrieved from public healthcare facilities for each month between January 2008 and December 2013. Flood water was mapped by month, in square kilometers, from satellite data. Poisson regression models with three lag months were constructed for the health problems in each district, controlled for seasonality and long-term trends. During times of flooding and three months after, there were small to moderate increases in visits to healthcare facilities for skin infections, acute respiratory infections, and diarrhea, while no association was seen at one to two months. The associations were small to moderate, and a few of our results were significant. We observed increases in care seeking for diarrhea, skin infections, and acute respiratory infections following floods, but the associations are uncertain. Additional research on previous exposure to flooding, using community- and facility-based data, would help identify expected health risks after floods in flood-prone settings.