Measurements of chemical persistence in natural environments can provide insight into behavior not easily replicated in laboratory studies. However, it is difficult to find environmental situations suitable for such measurements, particularly for substances with half-lives exceeding several weeks. The objective of this study was to demonstrate that a strategic postflood monitoring campaign can be used to quantify transformation half-lives on the scale of months in a real aquatic system. Water samples were collected in the upper Brisbane River estuary on 36 occasions over 37 weeks and analyzed for 127 pharmaceuticals and personal care products (PPCPs), pesticides, and perfluoroalkyl substances (PFASs). High quality time trend data were obtained for 41 substances. For many of these, data on the input of a wastewater treatment plant to the upper estuary were also obtained. A mass balance model of the estuary stretch was formulated and parametrized using PFASs as persistent benchmarking chemicals. Transformation half-life estimates were obtained for 10 PPCPs and 7 pesticides ranging from 18 to 260 days. Furthermore, insight was obtained into dominant transformation processes as well as the magnitude of chemical inputs to the estuary and their sources. The approach developed shows that under certain conditions, estuaries can be used to quantify the persistence of organic contaminants with half-lives of the order of several months.