Zone 2 extends northwards from Tamar Island to Swan Point in the mid to upper estuary.The waterway in this section begins to broaden with the widest point reaching over 3km in distance. The benthic habitat is predominately silt bottom (Lucieer et al., 2009) with the introduced plant species Spartina anglica (rice grass) and the introduced fish species Gambusia holbrooki (mosquito fish) both present within this area. The salinity and depth increases along the length of the estuary travelling north. Zone 2 had a salinity range of 0.5-24.5 ppt and a sampling depth range of 11-20 metres during the sampling period from October 2010 to September 2011. There are small communities spread out along the eastern and western shores of this zone with the largest being Legana and Exeter. Historically the dredge spoils from Launceston were deposited in zone 2 south of Windermere near the vast mudflats of Nelsons Shoal. There are also large sections of agricultural land along the eastern shore of this zone primarily used for grazing, cropping, orchards and vineyards.
Zone 2 experiences large and dynamic changes in salinity. The influence of freshwater inflows is reduced compared to Zone 1, however the surface water is always lower in salinity than the bottom, and winter rains result in lower salinities than drier summer months. As with Zone 1, there is interannual variability, and years with higher rainfall and more frequent flooding can result in significant differences in surface and bottom water masses. Zone 2 is the most dynamic zone in the estuary with respect to tidal marine influence and freshwater inflow.