Globally, scale deposition in water supply pipelines is one of the major problems faced by water utilities. This research aimed to determine the causes and effects of scale deposition in the water supply pipelines in Surakarta City, Indonesia. The total dissolved solids (TDS), hardness, manganese, and alkalinity in groundwater were higher than those in the surface water and spring water; thus, the supply areas from groundwater were identified using TDS at the taps. The three scaling indicators, i.e., the Langelier saturation index (LSI), the Ryznar stability index (RSI), and the Puckorius scaling index (PSI), indicated moderate calcium carbonate scaling. However, elemental analysis of eight scale samples using X-ray fluorescence (XRF) revealed that the major components of scale were either manganese (50.1–80.8%) or iron (45.6–63.8%), whereas calcium (3.0–7.8%) was a minor component. Because only five of twenty groundwater sources were chlorinated before distribution, it is estimated that dissolved manganese is oxidized by manganese-oxidizing bacteria. The manganese deposition rate in the networks was estimated to be 1660 kg/year using the manganese concentration at groundwater sources and in customers’ taps. These results suggest the importance of the elemental analysis of scale and avoidance of overreliance on scale indicators.