Environmental scanning electron microscopy (ESEM) with an energy-dispersive X-ray spectrometer (EDS) and time-of-flight secondary ion mass spectrometry (ToF-SIMS) were demonstrated to be useful analytical tools for investigating surface and bulk components of individual floc particles from both full- and bench-scale activated sludge systems. Detailed surface imaging of various hydrated biological floc particles by ESEM revealed substantial differences in surface features between treatment systems, while EDS identified spatial differences in the iron and the aluminum distributions. The ToF-SIMS spectra had signature fragments of protein and polysaccharide material from the floc surface, suggesting that this technique is capable of surface profiling extracellular polymeric substances. Principal-component analysis of the positive ion ToF-SIMS spectra from the mixed-liquor-suspended solid (MLSS) samples and reference aquatic organic materials found slight differences between the full- and bench-scale MLSS surface properties but substantial differences among MLSS and treated effluent from the same facility.