A variety of ecotechnologies have shown promising yet variable results in reducing faecal microbial contaminants under challenging operational conditions. But relatively limited work has been conducted to investigate and understand faecal microbe removal in these systems under highly fluctuating hydraulic and contaminant loading. In most instances, ecotechnology-based systems such as sedimentation ponds, constructed wetlands and bioretention filters have proved effective for treating episodic discharges and demonstrated performance resilience removing faecal microbial contaminants with modest to good efficiency particularly where inflow concentrations are high. However, microbial removal may depend greatly on the type of microorganism, treatment system design and operational factors. Design characteristics such as type of filter material and depth, presence of a submerged zone, type of vegetation and operational conditions such as inflow concentration, and antecedent dry periods in combination with temperature changes can all affect the removal of faecal microbes. Factors influencing survival, fate and behaviour of retained faecal microbes are still poorly understood. These knowledge gaps need addressing in order to fully evaluate microbial removal from fluctuating contaminated flows and more accurately interpret faecal indicator bacteria-based water quality and potential health risks associated with discharge from these ecotechnology-based systems