Understanding the process controls on episodic fluxes of faecal indicator organisms (FIOs) is becoming increasingly important for the sustainable management and accurate modelling of water quality in both recreational and shellfish harvesting waters. Both environments exhibit transitory non-compliance with microbiological standards after rainfall episodes despite significant expenditures on control of sewage derived pollutant loadings in recent years. This paper demonstrates the role of wave propagation in the entrainment of FIOs from river channel beds as a contributor to episodes of poor microbial water quality. Previously reported data is reviewed in the light of relationships between wave and mean water travel velocities. High flows and rapid changes in river flow, driven by releases of bacterially pure reservoir water, resulted in elevated FIO concentrations and transient peaks in concentration. The new interpretation of these data suggest three modes of entrainment: (i) immediate wave-front disturbance, (ii) wave propagation lift and post-wave transport at mean flow velocity, and (iii) stochastic erosional mechanisms that maintain elevated bacterial concentrations under steady high flow conditions. This is a significant advance on the previously proposed mechanisms. Understanding these mechanisms provides an aid to managing streams intended for recreational use and emphasises the need to control the timing of high flow generation prior to use of the water body for e.g. canoeing events. In addition the processes highlighted have relevance for the protection of shellfish nurseries, drinking water supply intakes and episodes of poor bathing water quality, and associated health risks.