Watershed-scale simulation models of microbial fate and transport are powerful tools that can be used for water quality management to address public health concerns. This chapter presents the various watershed-scale models that have been applied for modeling microbial fate and transport, their fundamental basis, recent applications, and model improvements. Both process-based models such as SWAT, HSPF, APEX, WAM, SWMM, WATFLOOD, GWLF, PCB, and RIVERSTRAHLER and non-process-based models like SIMHYD-ED and WALRUS are presented. Integrative models like FRAMES and QMRA and those that make use of other emerging approaches such as deep learning and inverse techniques are also covered. The extent of applicability, versatility, and simulation accuracy of the various models are then compared. Results showed that the SWAT and HSPF models are the most widely used and versatile models for microbial fate and transport, although applications exhibited varying degrees of accuracy. Future research and directions are recommended including more extensive field studies for a more accurate mathematical representation of the various microbial fate and transport processes, and the use of coupled surface and groundwater models, machine learning models, IoT and AI among others to enhance model predictive capabilities and broaden the applicability of these models for sustainable water resources management.