Subsurface flow ecotechnologies encompass a range of different designs, varying in terms of flow configuration, media type, energy requirements and use of wetland plants. This study compared the removal rates and internal dynamics of Escherichia coli in a range of commonly used and emerging subsurface flow systems designed for secondary treatment of domestic sewage. Fifteen pilot-scale units were loaded with primary treated sewage in Langenreichenbach, Germany and monitored at the inlet, outlet and a several internal sample points between August 2010 and December 2011. The compared systems spanned a range of energetic intensification levels, including passive horizontal flow (HF) beds (25 cm versus 50 cm deep), moderately-intensified unsaturated pulse-loaded (12 versus 24 times per day) vertical flow (VF) beds (gravel versus sand media), and highly-intensified beds with aeration (HF versus VF) or reciprocating fill and drain hydraulics. Planted (Phragmites australis) and unplanted forms were compared for all designs except for the reciprocating system (unplanted only). In general, there was no significant effect of vegetation on E. coli removal. Despite receiving the highest loading rates (131–146 L/m2 d), the aerated HF systems and the reciprocating system achieved the highest log concentration reductions (2.8–4.0 log10) and the lowest effluent E. coli concentrations (geometric mean less than 1 × 104 MPN/100 mL). The gravel-based VF beds had the lowest log concentration reduction (0.8 log10) and highest effluent concentrations (6.4–8.9 × 105 MPN/100 mL) at a hydraulic loading rate of 96 L/m2 d. The design type had an extremely significant effect on areal mass removal rates, with the passive HF beds having the lowest removal rates (50 cm depth significantly better than 25 cm), followed by the unsaturated VF systems (which were not significantly different from one another), while the aerated and reciprocating systems had the highest removal rates. Within the unsaturated VF beds, the use of sand versus gravel substrate, or hourly versus bi-hourly loading regime in the sand-based systems, had no effect on areal load removal. The internal concentration profiles were not significantly different between the unsaturated VF designs, with the exception of the hourly-loaded, planted bed with sand media which had a more rapid rate of concentration reduction with depth. In the HF beds, the internal E. coli concentration reduction was significantly faster in the aerated beds than in the non-aerated beds. Depth and plants had no significant effect on the internal concentration profiles within the non-aerated HF beds. Within the aerated systems, horizontal-flow achieved better E. coli removal than vertical-flow. Subsurface flow ecotechnologies offer great potential as robust and low-maintenance solutions for reducing the pathogen risk associated with domestic wastewater. The intensified systems produced effluent potentially suitable for restricted surface irrigation, at the cost of higher energy consumption, while the effluent from the other design types would require subsurface irrigation or further disinfection prior to reuse.