Hamilton Harbour has a new problem to add to its list of woes — goldfish.

Millions of tiny ones are swimming around after a summer that saw weather and water conditions turn Cootes Paradise into a massive breeding ground for the carp-like creatures.

The non-native fish species — that people buy as pets and sometimes, ill-advisedly, release into local waterways — have suddenly gone viral in the bay and have become the latest complication in its rehabilitation.

It used to be that goldfish in the Ontario outdoors had a very low survival rate and little success at reproducing.

But officials at the Royal Botanical Gardens and the Department of Fisheries and Oceans Canada say that's been changing in recent years in the warmer weather we've been experiencing.

They've noticed exponential increases in numbers being counted at the Desjardins Canal Fishway — from 20 or less per year in the late 1990s to 2,500 this past spring. And early this winter, millions of five centimetre, young-of-the-year goldfish have been seen swimming in giant schools at various locations in the harbour, including the section of the canal below the railway bridge.

"They seem to be heading toward taking over," says Tys Theysmeyer, the head of natural lands for the RBG.

Becky Cudmore, an invasive species expert with Fisheries and Oceans Canada, says it's a problem being noticed at numerous locations in the lower great lakes, with Hamilton Harbour being a particular hot spot.

"With increased warming trends we're seeing an increased ability of some fish species to survive in areas where we wouldn't think they could survive," she says.

Theysmeyer says low water levels in the early summer in Cootes Paradise — where fish tend to reproduce — that suddenly rose later on also assisted goldfish reproduction. Shallow water is good for eggs, slightly deeper water is better as the tiny fish start to swim around.

When water levels jumped 50 cms, doubling the volume of water, Cootes Paradise "basically turned into a goldfish factory," he says.

Most troubling, he says, is when the invading fish become fully grown. They can reach more than 40 cms in length, much smaller than mature carp, but big enough to cause similar damage to a fragile ecosystem.

Carp are destructive because they crowd out other species and are constantly churning up the bottom in their search for food. This inhibits the growth of plants and indigenous fish species.

The RBG has taken extensive steps to push them out of Cootes Paradise, most notably by using the fishway that operates like a gate for hand sorting of desirable and non-desirable species trying to return from Hamilton Harbour to Cootes in the spring. Those efforts have been largely successful.

But huge populations of carp remain in the harbour throughout the year and are a factor in discouraging the growth of desirable fish species such as pike and bass there.

Cudmore says this summer will be crucial in determining whether the goldfish flourish or not. It depends on the survival rate of the young of the year being witnessed now.

Maybe, she says, nature will respond and birds and bigger fish will step forward to chow down on the young plentitude. The enhancement in food supply could, in turn, help jump start desirable species such as pike and bass.

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Colin Lake, lead planning biologist with the Ontario Ministry of Natural Resources and Forestry, notes the province has been stocking walleye in the harbour since 2012 and young goldfish will definitely provide them an increase in food supply.

Goldfish in the bay have a variety of colour appearances from vibrant orange to dull grey. The brightly coloured ones will be the most vulnerable to predators, Cudmore says. Consequently, through time orange ones will likely be seen less frequently.

Cudmore urged people not to release their goldfish pets into the wild. "They might think they are doing a kind thing for the fish, but they are not doing a kind thing for the ecosystem," she says.