Abstract: Pathogen contamination in surface waters could cause outbreak of epidemics and threaten public health and it is usually indicated by Faecal coliforms (FC), a widely used measure of Faecal indicator bacteria (FIB). Bottom sediments harbor much high number of FC and are generally regarded as an internal pollution source. Their resuspension and settling often causes a change in concentration of suspended sediments (SS) and hence a change in the corresponding characteristics of FC partition to SS. However, the relationship of SS versus FC partition fraction remains yet unclear, and this has hindered a deep understanding of partition mechanisms and lowered the accuracy of microbial water quality models. In this work, experimental study and theoretical analysis were employed. Using experimental measurements we examined the impacts of sediment concentration on FC partition and developed a numerical model for the fate and transport of FC in sediment-laden flows, and then derived theoretical solutions for certain simplified cases. Lastly, we present a comprehensive analysis of the impacts on FC transport in overlying waters by FC partition, FC storage in bottom sediments, and intensity of FC movement near bottom water-sediment interface. The results show that a linear partition model can be used for describing the attachment of FC to suspended sediments. And the variation in FC partition fraction caused by different sediment concentration has a significant influence on the fate and transport of FC during resuspension and settling of bottom sediments. An increase in FC storage in bottom sediments or intensity of FC movement near bottom water-sediment interface will increase FC concentration in overlying water, and the former has a relatively greater influence on FC transport.