Measurement of elevated trace elements is an important component of environmental assessment and management of estuarine marine sediments in systems adjacent to concentrated human activity. The present study surveys the estuarine sediments in selected tributary bays, creeks, and the upper segments of the Georges River system, NSW, Australia, which flows into the Tasman Sea through Botany Bay. A total of 146 surface sediment samples were analysed by X-ray fluorescence. Potential pollution of sediments was evaluated using potential load index, modified degree of contamination, and potential ecological risk index. The spatial distribution of trace elements varies between sites. Variable sources of contamination, including runoff from catchment areas, and emissions from watercraft and boatyards are contributing sources. Bay morphologies and their interactions with catchment and tidal flows play significant roles in the distribution of trace elements. The greatest concentration of trace elements occurs around discharge points and in the inner parts of bays that have high percentages of mud particles and organic matter. The lowest contamination by trace elements was found in sandy sediments along the shoreline and edges of the bays. Trace element distributions decline in concentration in residential-free areas and reach background levels in deeper sediment cores. The concentrations of trace elements were controlled by discharge points from the catchment area, marine boat activities, bay morphology, and sediment types (sand, silt, and clay). The highest pollutant concentrations are the result of past legal, but uncontrolled, discharge of waste from manufacturing into Salt Pan Creek.