Rapid monochloramine decay has been observed in the product water of three River Murray water treatment plants (WTPs). Previous investigations identified that rapid monochloramine decay was microbiological in nature and observed in samples taken after media filtration but was absent in filtered water samples from a fourth WTP of similar design. The filters at the WTP not exhibiting rapid decay are backwashed with filtered non-disinfected water whereas the other WTPs backwash with treated chloraminated water. It was therefore hypothesised that backwashing filters with chloraminated water was the cause of the rapid monochloramine decay. A pilot-scale study was conducted to investigate the impact of backwashing with chloraminated water on the occurrence of microbiologically accelerated monochloramine decay. Additional samples were analysed to assess the impact of chloraminated backwash water on N-Nitrosodimethylamine (NDMA) formation and biological degradation of taste and odour compounds 2-methyl isoborneol (MIB) and geosmin in the filter media. Backwashing with chloraminated filtered water was concluded to be the cause of the observed rapid monochloramine decay, with rapid decay observed within 8 weeks for the filters backwashing with chloramines. Additionally, backwashing with chloraminated filtered water was observed to increase NDMA formation and impair the biological degradation performance of MIB and geosmin.