Salinisation in the Murray–Darling Basin, Australia, may affect aquatic flora and fauna, including the common carp, an alien species that has become the most common fish in the river system. This study describes the responses of juvenile carp (31–108 mm total length) to salinity levels that prevail in some wetlands of the lower reaches of the River Murray. Carp are moderately tolerant of salinity (direct transfer LC₅₀: 11 715 mg L^–1), particularly after slow acclimation (LC₅₀: 13 070 mg L^–1), but sub-lethal effects are evident at lower salinities. These include effects on osmoregulation (>7500 mg L^–1), behaviour (7500–12 500 mg L^–1) and sperm motility in mature fish (150–300 mm) (8330 mg L^–1). Salinities in some Murray–Darling Basin wetlands already approach half seawater (17 500 mg L^–1) and carp populations in these important nursery areas could be impacted through sub-lethal effects on adults and lethal effects on juveniles, eggs and sperm.