Many experiments, field measurements and few numerical tests shows the transport and fate of Faecal Bacteria have a tight relationship of the sediment transport including the absorbing, releasing and changing the radiation of sunshine especially in the fine cohesive particles and etc. The nonuniform distribution of 2-D and 3-D structures of hydrodynamic, salinity and suspended sediment (SS) in the riverine and estuary may make the solution of Faecal Bacteria to become more complex. With related measured data, the different coupling models based on modified EFDC 2D model are built to solve the dynamic processes of Faecal Bacteria and decouple the influences non-equilibrium transport of suspended and bed load sediment. The results in the Ribble river and estuary shows the sediment transport may have obvious influences on the Faecal Bacteria processes with ranged about maximum 10~30% variance in the shallow Ribble delta region. In addition, the sediment deposition and erosion driven by the different hydrodynamic condition may cause the accumulative impact on the Faecal Bacteria processes and cause a fluctuation at some degree on the dynamic distribution of FIO concentration.