The Brisbane River estuary, Queensland, Australia, is a vital ecological region and of importance for people who live nearby. The estuarine health status has been influenced by both marine and riverine conditions. The estuary experiences high turbidity and salinity throughout most of the year, however, little is known about the actual turbidity and salinity structures within it. This study examined ten-years of field data to investigate the seasonal variations in salinity and turbidity. The results revealed that the salinity at the Brisbane River mouth was estimated to be 31.7 and 32.8 ppt during wet and dry seasons, respectively. The surface longitudinal salinity then decreased along the estuary, with the highest decreasing rates of 0.7 and 0.6 ppt/km occurring within the mid-estuary. The average salinity flux was 8.19×104 and 8.25×104 ppt m3/s during the wet and dry seasons, respectively. The slight discrepancy of salinity fluxes between two seasons may be attributed to the lack of consideration of the other freshwater inflows to the estuary. The actual salinity flux through the estuary will therefore fall within the two estimated flux values. It was also found that the length of the turbidity maximum was approximately 35 km during wet season, which was three times as long as it is during the dry seasons. The values indicate the perceived, and actual, health of the estuary changes with season and location and thus care must be taken when interpreting ad-hoc measurements.