Scientists say the extra water has resulted in significant reductions in both salinity and nutrient levels triggering a boom in aquatic life.
There has been a substantial increase in fish including congolli, black bream, greenback flounder and yelloweye mullet which has also brought more birds to the region.
The Coorong's underwater plants, including many almost lost from the system during the drought from 2001 to 2009, are also recovering.
The South Lagoon, which was severely impacted by the millennium drought appears to be bouncing back with reduced salinity and increased animal life including macroinvertebrates.
South Australian Research and Development Institute principal scientist Qifeng Ye said species numbers had doubled in the South Lagoon as salinity levels fell to less than 60 grams per litre.
"The increase in fish biomass will also now benefit the many fish-eating birds and larger fish within the waters," Professor Ye said.
The upbeat assessment of the region has been provided by scientists engaged to analyse water quality through the Healthy Coorong, Healthy Basin program.
"This important scientific work is yielding wonderful news for the ecology of the lakes," Environment Minister Susan Close said.
"While the floods have provided a much-needed boost to the Coorong and Lower Lakes, it must be sustained into the future through sufficient environmental flows.
"The Coorong and the Lower Lakes were the absolute last refuge for birds and other animals throughout the drought and we must continue to ensure it is there when the next big dry spell hits."
Summer's flooding down the Murray brought water levels not witnessed across the river system for more than half a century.
About 4000 properties, including shacks, homes, and businesses, were impacted to varying degrees with hundreds of roads closed for several months.
Water levels peaked in the state's Riverland at Christmas and in the lower reaches in early February. They have since dropped back significantly allowing a major clean-up across river communities.