This study presents investigations on microbiological water quality numerical modelling. Emphases have been laid on the model development by implementing state-of-the-art technologies in terms of the new research branch in water science, established in 1980s - hydroinformatics. In the study, new mathematical equations for modelling bacterial re-suspension from bottom sediments and disappearance due to sediment deposition are established. Therefore, the bacterial re-suspension from bottom sediments is firstly modelled. The bacterial sedimentation equations presenting bacterial disappearance due to sediments settling process in natural waters is also introduced, which is independent from the well- known first order decay model. Based on the new equations, an integrated 1-D and 2-D hydroinformatics water quality simulation model has been developed, carrying out sediment transport associated bacteriological water quality modelling. The model therefore performs modelling work including hydrodynamic modelling, sediment transport modelling and bacterial decay modelling which is associated with the sediment transport processes. The new bacterial decay model encompasses the terms of bacterial first order decay, bacterial resuspension and the bacterial deposition. Object-oriented methodologies are employed in the integration of the sediment-associated multi-dimensional water quality model to encompass well-tested existing modules, by implementing Fortran 90 and Visual Basic 6.0 programming languages to deploy the advanced numerical schemes and provide a state-of-the-art GUI system. Validation and calibration of the integrated sediment-linked water quality model has been carried out in its application to the Bristol Channel and Severn Estuary by using vast volumes of data from in-situ field measurements including: diffuse faecal indicator sources of 29 riverine inputs point faecal indicators sources of 34 WwTW outfalls daily- recording hourly observed sunlight radiation data downstream real-time tidal water elevation boundary data upstream Severn River flowrate variations and the bathymetry data across the 1-D and 2-D domain. Satisfied calibration results were obtained and the model was successfully validated to estimate the enterococci concentration levels at beach bathing water compliance locations, thereby could now be applied to other estuarine environments.