The distribution of salinity, temperature, suspended particles, light transmissivity, chlorophyll a and phaeopigments across the Great Barrier Reef lagoon offshore Townsville, was measured from 9 January 1979 to 23 January 1980 at approximately weekly intervals. Previous observations at Low Isles. 400 km to the north, on seasonal variations of temperature and salinity were generally applicable here. A shallow summer thermocline was frequently observed in offshore waters, in the dry season and in calm weather. As a result of evaporation from the lagoon and adjoining mangrove swamps during the dry season, an inverse estuarine circulation can exist when high salinity, sediment-rich, nearshore waters sink below the less saline offshore waters. Only nearshore were bottom sediments strongly entrained in the water column during strong winds, principally in winter.