Estuaries act as nurseries for many penaeid prawns, but these habitats are highly susceptible to salinity decline through flooding. The rate of salinity decline and duration of exposure to non-optimal salinity may affect survival and subsequent recruitment of prawns to the fishery. This study aimed to determine the effect of salinity fluctuations observed in local estuaries during flood events using a novel dilution approach. Mortality of juvenile Melicertus plebejus (Hess) was assessed after 24 hr exposure to 24 rates of salinity decline ranging from 0.01% to 20% per hr. After the salinity decline, prawns were held at the final salinities for five days before again assessing mortality as well as aerobic metabolic rate and prawn water content. Salinity decline from 36 to ~0.8 led to 50% mortality, but continued exposure to low salinity for five days increased mortality at this salinity to 99% and shifted the 50% mortality point to salinity ~5. Aerobic metabolic rate and water content data suggested the cause of mortality due to exposure to salinities < 5 was osmoregulatory failure. Rapid salinity declines over 24 hr and sustained low salinity due to flooding could compromise the survival of juvenile prawns, potentially reducing recruitment to the fishery.