The sediments range from organic silts to sands.¹⁵ The surface few centimetres have relatively high nutrient concentrations, and are bioturbated through the activities of amphipods and annelids. They are also readily resuspended through wind-induced wave action, and the effect is well seen for shallow sites with a long fetch (Figure 5). Rates of deposition into sediment traps reach 234 g m² day^-1 in Harvey Estuary, and this is very largely because of the deposition of resuspended sediment.¹⁶   Such resuspension occurs frequently, and is relatively more significant in Harvey Estuary than in Peel Inlet because of the orientation of the long axis of Harvey Estuary in relation to the prevailing wind direction, and also because of the less dense, organic-rich sediments there. The turbidity brought about by resuspension in Harvey Estuary, together with dense algal blooms for part of the summer, combine to reduce light at the sediment surface to the point that growth of benthic macroalgae are essentially precluded except at the far north of the estuary.¹⁷In contrast, sufficient light penetrates to the sediment surface in Peel Inlet to allow the growth of macroalgae, especially on the broad, shallow marginal platforms.¹⁸

Another feature of the sediment surface is the presence of relatively high populations of microphytobenthos, as measured by chlorophyll a concentrations.¹⁹ These algae offer the potential for high rates of benthic photosynthesis and could affect nutrient exchange between the sediment surface and overlying water. Resuspension of benthic algae, especially pennate diatoms, accounts for much of the chlorophyll recorded in the water column in late summer in both basins.

The sediments are both a source and sink for nutrients. Wind-induced resuspension of sediments provides an opportunity for sediment phosphate adsorption to occur, but in our experience a subsequent period of stratification and consequent oxygen reduction is sufficient to allow phosphate release from the sediments once again. Diatom blooms in winter are responsible for the trapping and sedimentation of nutrients; it was calculated for a single winter river inflow event that of the phosphorus arriving over a period of 18 days (some 80% of which is in the form of filterable reactive phosphate), 71 % was trapped in a rapidly developing diatom bloom.²⁰

The winter diatom bloom has two effects - one is to trap phosphorus, and the other is to load the sediments with a source of respirable carbon which drives the sediment surface anaerobic and allows subsequent phosphate release. If sediment cores collected from the estuary are incubated in darkness in the laboratory, and phosphate concentrations are measured in the water above, then large seasonal and between-year differences are observed (Figure 6). These differences are attributed to differences in the nutrient loading between years and the consequent occurrence of winter diatom blooms. In years with little nutrient loading and no diatom bloom, there was no subsequent nutrient release. In other years there was considerable nutrient release (up to 190 mg P m^-2 day^-1), and release continued during and after the occurrence of blue-green blooms in summer.^10,21 The effect of the diatoms on nutrient release has been demonstrated experimentally in the laboratory (Figure 7).

There are large year-to-year differences in the magnitude of the summer Nodularia blooms, and these differences are related closely to the volume of river flow in each previous winter, and so to the nutrient loading in that winter.^10,14 This is attributed to the magnitude of diatom blooms and nutrient cycling from the sediments. Thus the size of a Nodularia bloom in summer depends not so much on the total nutrient pool accumulated over the long term in the sediments, but whether or not conditions are favourable for nutrient release in a particular year. This has important management implications.

Like the blue-green algae, the macroalgae in Peel Inlet (see below) grow mainly in the summer months, when ambient nutrient concentrations are low. They too depend on the recycling of nutrients from sediments and decaying masses of algae. The anaerobic conditions beneath banks of algae favour nutrient release, and the nutrients promote macroalgal growth where light is not limiting.²²