Aquaculture in Tasmania is mostly carried out in estuaries. These estuarine habitats show a great variety and form unique environments in which Neoparamoeba pemaquidensis, the amoebic gill disease (AGD)-causing protozoan, may or may not survive. Tasmania is divided into two zones, one where AGD is present and one where AGD is absent, but any ecological data to rationalize this distribution is lacking. In in vitro trials N. pemaquidensis strains were exposed to different concentrations of ammonium sulphate, copper sulphate, copper sulphate and tannin, and different Neoparamoeba densities, salinities and temperatures. A trial using field water samples investigated the survival of N. pemaquidensis in waters sourced from AGD-free and AGD-positive zones, and water analysis was performed to determine any differences. Significantly decreased protozoan survival was found with exposure to increasing copper sulphate concentrations from 10 to 100,000 microM (P < 0.001), salinity of 15 per thousand (P < 0.001), low Neoparamoeba densities of 625 and 1,250 cells mL(-1) (P = 0.0005), and water sourced from Macquarie Harbour (P < 0.001). The water chemistry of this AGD-free zone showed significantly lower dissolved calcium and magnesium concentrations which may contribute to this area being AGD-free. Understanding of the ecology of N. pemaquidensis will enable better control and prevention strategies for Tasmanian salmon growers.