Field studies were conducted in a Croatian city supplied by two distinct groundwater sources (referred to as A and B) to investigate both the effects of changing water source on the water quality in the drinking water supply system, as well as to further understand discoloration events that occurred in city locations that switched water from source A to B. The water treatment processes at site A were found to alter organic matter (OM) characteristics, removing humic substances while enhancing protein-derived (tryptophan) content. Although the humic-like component predominated in raw waters, microbially/protein-derived components were found to increase throughout the distribution networks of both systems. Disinfection byproducts (DBPs) such as total trihalomethane (TTHM) and total haloacetic acid (THAA) were prevalent in water distribution system (WDS)-A, which correlated with elevated OM content as well as re-chlorination with hypochlorite (NaOCl). Our field study revealed that THMs were more readily formed than HAAs during ClO2 treatment. Unsurprisingly, chlorite concentrations were generally higher than chlorate concentrations during ClO2 treatment, whereas (secondary) NaOCl disinfection contributed to higher chlorate production. Principal component analysis indicated that variable pH values and humic-like OM could affect Mn, As and Al concentrations at the consumer's tap. Our results suggested that although Mn concentrations complied with regulations at WDS-B and were below 50 μg/L after disinfection, Mn was oxidized and formed particulate Mn oxides capable of causing discoloration events depending on prevailing network physico-chemical and hydraulic conditions. Aluminium also appears to be released during hydraulic disturbances from extensive deposits within the network. Thermodynamic calculations showed that Mn-oxidation was strongly dependent upon the ORP, and to lesser extent the pH value. Collectively, our results confirm that ensuring the provision of safe drinking waters to consumers requires an understanding of water quality across entire distribution networks in addition to any routine post-treatment monitoring.