Escherichia coli and other enteric pathogens presence indicate that the water has been contaminated with fecal matter. River deltas are population hotspots which are becoming increasingly urbanized and where poor sanitation has been frequently identified as a pressing issue. In this study, we have investigated the spatial distribution of E. coli in river deltas under varying river discharge, temperature and irradiation at the water surface. A hydrodynamic and water quality model has been used to reproduce an idealized river delta configuration and to investigate the spatial distribution of E. coli across the delta floodplain and channels. The concentration of E. coli rapidly declines downstream, following a tripartite trend with different decline rates on the delta front, pro-delta and shelf area. The highest differences in the spatial distribution of E. coli bacteria occur for low-river discharge values. Temperature and irradiation both influence the concentration of E. coli and mostly influence downstream areas and smaller channels.