An acoustofluidic device has been developed for concentrating vegetative bacteria in a continuous-flow format. We show that it is possible to overcome the disruptive effects of acoustic streaming which typically dominate for small target particles, and demonstrate flow rates compatible with the testing of drinking water. The device consists of a thin-reflector multi-layered resonator, in which bacteria in suspension are levitated towards a glass surface under the action of acoustic radiation forces. In order to achieve robust device performance over long-term operation, functional tests have been carried out to (i) maintain device integrity over time and stabilise its resonance frequency, (ii) optimise the operational acoustic parameters, and (iii) minimise bacterial adhesion on the inner surfaces. Using the developed device, a significant increase in bacterial concentration has been achieved, up to a maximum of ~60-fold. The concentration performance of thin-reflector resonators was found to be superior to comparable half-wave resonators.