Healesville Sanctuary life sciences curator Russel Traher said ecosystems starved of water in the past five years had been thriving since downpours started on September 26.

"It's pretty amazing just walking around the property here to see how much plants have grown - it's great to see water gushing down Badger Creek."

The wet weather has rejuvenated the natural food cycle with plants and insects providing a greater food source for hatchlings and young animals coming out of nests.

Mr Traher said helmeted honeyeaters, critically endangered in Victoria, benefited greatly with swamp lands now flooded and recharged.

"This year so far the number of honeyeaters coming out of nests has been promising."

Melbourne Water reported the downpours led to the highest spring river flows since 2004 and created the best breeding conditions in years for platypus, native fish and frogs.

Melbourne Water's manager of waterways, Chris Chesterfield, said waterways had been doing it tough for the past five years and animal populations had been affected.

"Minor floods are a critical part of river ecology. They trigger fish to spawn, flush sediment and carve out new ponds and habitats. These are some of the best conditions we've seen in the Yarra in nearly five years."