Scanning electron microscopy and X-ray energy spectroscopy (SEM/XES) were used to survey the biological and nonbiological particles in two different municipal driking-water systems. Microbiological particles could be differentiated from non-biological by their qualitative elemental compositions and this information was used as the basis for an automated detection scheme. Automated SEM/XES analyses were used to demonstrate microbiological differences between well-water and surface-water in distribution systems.