While agricultural activities, such as the application of manure on arable land and animal grazing on pastures, provide economic and environmental benefits, they may also pose microbial risks to water sources. The aim of this paper was to study the microbial fate and transport in an agricultural catchment and recipient water source through further development of the hydrological model HYPE. Hydrological modelling was combined with hydrodynamic modelling to simulate the fate and transport of Salmonella spp., verotoxin-producing Escherichia coli O157:H7 (VTEC) and Cryptosporidium parvum in an agricultural catchment of a drinking water source, Lake Vombsjön, in Sweden. This approach was useful to study the influence of different processes on the pathogen fate and transport, and to interpret the relative changes in the simulated concentrations. Sensitivity analysis indicated that the largest uncertainties in the model were associated with the estimation of pathogen loads, parameterisation of the pathogen processes, and simulation of partitioning between surface runoff and infiltration. The proposed modelling approach is valuable for assessing the relative effect of different risk-reducing interventions.