Changes were assessed in urban wastewater treatment plant (WWTP) effluent quality during short-term storage in open surface ponds. Water quality was monitored over five years at the inlets and outlets of open storage ponds located at three biological nutrient removal plants. Pond influent temperature, rainfall and sewage inflow were not found to be major factors. However, there was a trend for water temperature to be correlated negatively with nitrogenous nutrient and positively with faecal coliform values. The observed increases in faecal coliforms, nutrients and chemical oxygen demand were most likely caused through avian faecal contamination. These increases challenge the notion that pond storage has a positive or negligible effect on effluent quality. The observed one to two orders of magnitude increase in faecal coliforms may affect reuse scheme viability by limiting the range of uses under Australian water recycling guidelines. Potential improvements to short-term recycled water storage management at WWTPs could include the integration of monitoring requirements in WWTP discharge licences and recycling guidelines and the monitoring of all water quality parameters, including microbiological ones, at the point of entry into the recycled water distribution system, after WWTP storage, rather than directly post-disinfection.