This dataset describes data collected from the Huon Estuary (Tasmania). Data was collected over a three day period approximately every three months from March 1996 until August 1998. 10 surveys were completed (HES1 to HES10). Data was collected from 61 sites, ranging from 0 salinity at Judbury to a salinity of 35 at the seaward end of the estuary near Huon Island. 5 sites were located near fish farms (refer to the separate metadata record for weekly data at these sites). At these sites, data was collected for all parameters (CTD, salinity, dissolved oxygen, nutrients, pigments, spectral absorbance and phytoplankton) measured. At a further 31 sites spread over the estuary, data was collected for the physical and chemical parameters only. At the remaining 25 sites, only physical (CTD) data was collected. Below Port Huon, samples were collected at three depths - surface, fluorescence maximum and from within the salt wedge. Above Port Huon, samples were collected from the surface and from the salt wedge (where present). This dataset forms part of the CSIRO Marine Research Huon Estuary study, conducted over the period 1996-1998.