This paper presents results from a preliminary assessment of phosphate-loaded sediment occurrence and distribution of the Johnstone Rivers system, in the Cairns section of the Great Barrier Reef Marine Park. Total PO4 concentrations in channel sediments show a substantial increase from rainforest to agricultural settings and inorganic PO4 concentrations are much higher in the tributaries draining agricultural land than in either main river. It was also found that total PO4 concentrations are much higher in the dry season than in the wet season. The results of this study indicate that agricultural practices have a noticeable influence on the PO4 content of riverine and estuarine sediment of the Johnstone Rivers. Despite this, the estuarine, offshore and reef sediment data suggest that the phosphate loss from agricultural land in the Johnstone Rivers catchment is unlikely to affect the nutrient status of the Great Barrier Reef. Reworked, fine-grained phosphate-bearing sediment may, however, have an impact on nearshore marine ecosystems.