The scale of ex-Tropical Cyclone Jasper and resulting flooding has conservationists anxious about the impact on local wildlife and the nearby Great Barrier Reef.
Immense amounts of rain that fell on the area can affect the salinity of waterways, create toxic run-off and displace fauna.
Wildlife veterinarian, Dr Claire Madden said the loss of pristine habitat could be one of the more devastating and ongoing impacts of the floods.
"Cairns and that Daintree Rainforest area is just such a hotspot for birds, reptiles, marine life," she told AAP.
"The impact it's going to have in the weeks coming ahead is going to be pretty catastrophic."
Great Barrier Reef campaigner with the Australian Marine Conservation Society, Tanya Murphy said early reports suggest the most heavily visited parts of the reef appear to have escaped immediate severe damage from Jasper.
"The state of the reefs further north remain to be surveyed, but the reefs near Cairns and Port Douglas appear to have been relatively lucky this time," she told AAP.
Impacts may be delayed however, as debris, silt and general rubbish washed into coastal waters smother marine environments like sea grass and coral.
"This in turn can impact animals like dugongs and turtles which feed on seagrass, and species which rely on coral reefs for their food and shelter," Ms Murphy said.
"Many marine species start their life cycle in mangroves and river mouths before heading out to the Reef so if those nurseries have been impacted by the floods, we won’t see the impacts on those populations until later."
With waters now receding, the bulk of animal rescue and rehabilitation efforts will take place over Christmas and the new year.
"Usually with flooding we see a lot of wildlife pushed out of their normal habitat," Dr Madden said.
"They don't know where all their resources are like food, water, shelter, those sort of things.
"We see a lot of emaciation and starvation cases in the days to weeks that follow."
Even those that already live in the water such as crocodiles and turtles can suffer from their salt water environments becoming too diluted and turning to fresh water.
"We see a lot of impacts on all of our marine species because they can't live or survive long-term with those low salt levels," Dr Madden said.
"The immediate impacts we're going to see in the next few weeks, but there's potentially months or even a couple of years where we're going to see it really affecting wildlife up there."
Residents are being told not to take it on themselves to help injured or struggling wildlife they come across, but to call in expert help.