The management of livestock, and their manure, in agricultural landscapes provides a source of microbial pollution in the environment. With an increasing frequency of storm events there is greater potential for diffuse microbial pollution entering surface waters, which can threaten important ecosystem services linked to clean and safe water. However, diffuse sources of microbial pollution are difficult to manage as their loading and connectivity varies so widely across the landscape. SCIMAP is currently optimised to predict the risk of diffuse pollution (such as fine sediment and nutrients) to receiving waters at the catchment scale. Diffuse microbial pollution provides a new challenge for the SCIMAP framework. Faecal indicator organisms (FIOs) are organisms which provide an internationally accepted surrogate measure of faecal pollution. Here the SCIMAP fitted approach is applied to a dataset of FIO concentrations from two catchments; The River Yealm in Devon, and the River Wyre in Lancashire. The performance of SCIMAP in its prediction of diffuse FIO pollution was variable and much uncertainty was associated with the assignment of land cover risk weightings. The experiment highlights opportunities for the gathering of new knowledge and data which will be essential for the improvement of SCIMAP’s treatment of diffuse microbial pollution. Here we discuss the potential existing knowledge has in improving SCIMAP’s performance as well as current and future work which may provide opportunities for the improvement of SCIMAP’s treatment of the fate and transfer of FIOs in the environment.