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Myall Lakes is a large brackish coastal lake on the east coast of Australia that was considered pristine until the occurrence of blue-green algal blooms in 1999. The temporal and spatial extent of chemical and biological changes to the water column of Myall Lakes was studied intensively after a rain event in 2002. Water quality profiles (T, EC, pH, DO), turbidity (secchi), nutrients (TN, NO x , NH4 +, DON, TP, FRP, DOP, Si), and phytoplankton (chl a and cell counts) were measured at nine sites on eight occasions immediately after the rain event. Freshwater inflows affected a large area of the lake. Greatest changes were seen in areas close to the mouth of the upper Myall River which is the largest freshwater input to the lakes. Here, greatly elevated concentrations of NO x , TP, and FRP (up to two orders of magnitude higher than background) were recorded immediately after the rain event but persisted for only 2 to 8 days. Slightly elevated concentrations of TP and NO x were seen in inflows from the smaller Boolambayte Creek. Stratification was associated with bottom water anoxia and release of ammonia from the sediments. Identification of the sources of nutrient species delivered from different parts of the catchment, combined with studies of nutrient loads can assist managers to develop effective nutrient reduction strategies to reduce the incidence of blue-green algal blooms in Myall Lakes. [ABSTRACT FROM AUTHOR]