Sediments delivered to freshwater and marine environments can make important contributions to the aquatic bioavailable nutrient pool. In the Great Barrier Reef (GBR) catchments, particulate nutrients comprise an important fraction of the end of catchment loads; however, their contribution to the bioavailable nutrient pool is not well understood. This research determined which particulate nutrient parameters are the best indicators of the potential effect of fine sediment (<10 μm) on phytoplankton growth. Surface and subsurface sediments were lab-generated to cover a wide spectrum of particulate nutrient bioavailability from key soil types, land uses and erosion processes (hillslope and gully) in a wet and a dry tropics catchment of the GBR. Phytoplankton bioassays were used to assess freshwater and marine phytoplankton responses to sediments. The best indicators were selected by regressing measurements of phytoplankton growth against nutrient bioavailability parameters measured on the sediments. The selected indicator equations included organic carbon (C) pools for both fresh and marine water, highlighting the role of bacteria in mediating nutrient availability for phytoplankton. The equations also included various fractions of particulate nitrogen (N) (differentiating the adsorbed ammonium-N from the particulate organic N), and the ratios of C to N, which indicate the lability of the organic matter present in the sediment. Dissolved reactive phosphorus was also an important indicator in freshwater. The indicators performed better in assessing bioavailability potential than traditional methods to monitor particulate nutrients, e.g., particulate N and particulate phosphorus. Phytoplankton bioassays indicated that nutrients in sediment can promote phytoplankton growth, with nutrient bioavailability depending not only on sediment load, but also sediment characteristics associated with its parent soil. These characteristics vary with soil type, land use and erosion process. Findings will help prioritize erosion control to catchment areas which are most likely to contribute large amounts of bioavailable particulate nutrients to the GBR.