The purpose of this study was to determine whether there was a sufficiently high residual salt load in the dry sediments of the St Lucia Estuary to cause salinity problems should it later fill up with either freshwater or seawater. The estuary lakes have suffered the effects of a severe drought since 2002 with the result that many areas were dry, and the salinity of the residual water varied between 4 psu and up to five times that of seawater. Measurements of the salts content in the sediments to a depth of 20 cm showed that more than 2 million tonnes of salt was held in this layer of the sediment in 2006. Recent management of the estuary (since 1970) has ensured that the mouth was not artificially opened. This was to prevent the inflow of seawater, with its salts, that would otherwise enter while the drought was in place. The results of the sediment salinity data showed that if the drought had been broken and the lake area filled with rain and river water, the resulting salinity would be about 6 psu. In March 2007, Cyclone Gamede in the Indian Ocean off the east coast of South Africa produced a wave climate at sea that resulted in the mouth breaching; thus introducing an estimated 12 million tonnes of salts. The high salinity in the system resulting from this breach is expected to have an adverse effect on the ecology of the system, whereas the residual salinity in the sediments would not have caused an environmental problem. If the estuary and lake system were to fill completely with seawater, the residual salts together with seawater will raise the salinity to an initial value higher than 40 psu, which will have the effect of suppressing much of the important submerged vegetation that is vital for sustaining juvenile fish in the system. Many of the large fauna will also suffer from a shortage of freshwater.