Because of eutrophication problems in the system, there has been an ongoing study of nutrient concentrations and their implications for management. These investigations began in 1977, but were intensified in 1978 in a collaborative, 2-year study designed primarily to discover interrelationships between concentrations at different sites in the inlet,  and this study carried out at seven sites at fortnightly intervals established that river flow  was the only significant exogenous source of nutrients for the inlet.⁸   Monitoring of water quality then continued at weekly, fortnightly and (more recently) at somewhat longer intervals in summer. It was found that mean nutrient concentrations for three sites in each inlet did not differ significantly from means calculated using data from eight and seven sites, for Peel Inlet and Harvey Estuary, respectively,¹⁴ and it is the mean for the three sites which is described below.
 

Concentrations of nutrients differ greatly at different times of year, and between years (Figure 4). Nitrate rises sharply at the time of river flow. and especially during heavy flows of the Murray River, when nitrate concentrations (NO₃-N) may reach 33 mg L^-1 in surface water in Peel Inlet.¹⁰ when it is stratified. At other times of year, nitrate may rise sharply because of nitrification following the decomposition of organic matter in the estuary. Ammonia concentrations are not high in river water, but are mainly generated in the system through decomposition, for example in the estuary in winter or following the collapse of blue-green algal blooms in summer.

Phosphate concentrations (PO₄-P) are generally low (<10 ug L^-1) in the inlet, until the time of river flow; concentrations then increase, especially in Harvey Estuary. However, concentrations then fall rapidly to very low figures and generally remain low throughout the summer period.
 

Total phosphorus and total nitrogen concentrations are generally high and erratic, but are especially high during the time of Nodularia blooms because of the large amounts of nutrients associated with the high biomass. Much of the variability at other times is due to wind stirring, which, as explained further below, readily brings the surface sediments into suspension in this shallow system.

One of the striking features of the system is that nutrient concentrations are generally low until times of river flow, yet the macroalgae and blue-green algae grow most rapidly in the warmer months. This provides circumstantial evidence that nutrients must be trapped in winter and recycled via the sediments to support the development of a high biomass in summer. This recycling is reviewed in greater detail below.