We describe effects of salinity and temperature on germination characteristics of three dominant macrophytes, Phragmites australis, Juncus acutus, and J. kraussii, located in wetlands along the Hunter River, New South Wales, Australia. These wetlands were altered, from estuarine to freshwater habitats, by flood mitigation activities initiated during the 1970s. Tidal restoration to approximately 300 hectares of the marsh is planned to occur by 2008, with the goal to reduce freshwater vegetation in favor of salt marsh species. We determined if timing restoration projects to coincide with natural germination cycles or seasonal conditions of high salinity would be disadvantageous to P. australis or J. acutus germination. Germination trials lasted 25 days under two temperature range treatments (l0–25 and 15–30°C) and a salinity gradient (0–30 ppt). Many P. australis seeds commenced decomposition after three days (up to 58%). Increased salinity lowered germination in all species; however, only P. australis was influenced by temperature. Phragmites australis germinated in all conditions, although germination rate was low (2% ± 1.7) in the highest salinity treatment at high temperature regime. Both Juncus species obtained 100% germination in freshwater, failed to germinate in the highest salinity, and seed viability was not affected by 25 days emersion in high salinity. For areas dominated by P. australis in eastern Australia, we suggest that tidal reinstatement should be initiated in late autumn when P. australis seed banks are low. Additionally, periods of heavy rainfall, which reduce soil salinity, may help other species colonize the area. Further studies are required to determine characteristics of J. acutus that can be used to repress the species spread along the eastern coast of Australia. Currently, active measures involving chemical and physical weed suppression, litter removal, and mass planting of native species, are likely to be required to achieve management goals.