Stream sediments have been recognised as an in-channel store of faecal contamination that can be mobilised during floods or other sediment-disturbing events. We studied this store of faecal contamination by creating artificial floods during dry weather when, in the absence of overland flow from the catchment, the only source of faecal bacteria was stores within the channel. Artificial floods, created by releasing water from a supply reservoir, increased the E. coli concentration in the water column by two orders of magnitude, from a background level of 10(2) cfu per 100 mL to over 10(4) cfu per 100 mL. The bacterial peak concentrations and yields declined systematically through a triplicate flood series. The size of the total in-channel store, calculated as the sum of yields of an infinite series of artificial floods, was approximately 10(8) cfu m(-2) of streambed area. Direct measurements of sediment E. coli found few sites (only those associated with cattle crossings) with areal concentrations as high as 10(8) cfu m(-2), consistent with flood yields. Concentrations of E. coli in the biofilms on exposed rocks were orders of magnitude lower, indicating that exposed rocks were not a source of E. coli released by the artificial floods.