Flocs are irregularly shaped suspended particles of complex structure and composition that occur naturally in aquatic systems. In water treatment facilities, the settling of flocs is extremely important. Transmission electron microscopy was used to quantify the formation of a nanoscale surface layer on flocs from two laboratory bioreactors modelling a biological wastewater treatment facility. By comparing different floc populations, we demonstrated that flocs that settled quickly out of wastewater had a significant amount of this layer, whereas those with little nano-scale surface layer had poor settling properties. This morphological feature of floc ultrastructure may permit engineering manipulations that promote floc settling.