Waste stabilization ponds (WSPs) are used extensively for the treatment of wastewater in Australia, mostly in regional and remote areas. Wastewater treatment plants (WWTPs) using pond technologies are also distributed over the full geographical extent of Australia, encompassing many climatic zones. Predominantly used to service small to medium‐sized communities, WSPs are also used to service large metropolitan Australian populations, up to 2.5 million people. When well‐maintained, WSPs are a sustainable and resilient treatment option, and treatment is achieved at significantly lower cost when compared with conventional WWTPs. Increasing population, changing regulations, and climate variability are placing increasing pressure on Australian WSP systems. Sludge accumulation over time presents a significant challenge to pond maintenance, along with increasing occurrence of toxic cyanobacterial bloom events. These challenges are only enhanced by the wide geographical distribution and by increasing operational and maintenance costs. Increased demand for recycled water is placing further pressure on Australian WSP systems, as higher value treated water is expected from WSP infrastructure that is often overloaded or under‐designed. This increased demand for high‐quality treatment presents an opportunity for operators and researchers to develop a better understanding of the coupling between hydraulics and microbial ecology of these systems. With more stringent guidelines for greenhouse gas emissions (GHGs), a better understanding of biophysicochemical processes in WSPs will lead to better estimates of GHG fluxes and variability. This information will become critical for the future planning, maintenance and operation of WSPs, and will result in a better understanding of WSP systems overall.