Accurate synchronous measurement of salinity and sediment concentration has always been a concern for estuarine researchers. Considering salinity measurement based on electrical conductivity and sediment concentration measurement based on optical backscatter are still the most widely used measurement methods, a set of salinity measuring instrument and a set of fibre optic sediment concentration measuring instrument are designed and developed in the paper. The mutual influences between synchronous measurement of salinity and sediment concentration are experimentally studied. The experimental results show that the presence of sediment decreases the measured value of salinity, and the presence of salinity decreases the measured value of sediment concentration. The correlation relations and the corresponding correction formulae are determined experimentally. The proposed method improves synchronous measurement accuracy of salinity and sediment concentration, which is of great significance for their accurate measurement in estuarine coastal waters.