Marsh Recovery, Declining Fish Population: 30 Years of RBG Fishway Data

By David Galbraith, Director of Science, and Jennifer Bowman, Senior Ecologist of Aquatic Conservation

Saturday, May 23, 2026 is World Fish Migration Day, a biannual global event celebrating the remarkable journeys fish make between spawning grounds and open water, and the work required to keep those routes open.

As part of long-term programs to restore the ecology of Hamilton Harbour, Royal Botanical Gardens (RBG) has been monitoring fish moving into Cootes Paradise Marsh for three decades at the Cootes Paradise Fishway. Carp numbers are down, aquatic plants are coming back, and the proportion of native fish passing through the Fishway has climbed from roughly 20 per cent in the late 1990s to more than 90 per cent today. The marsh is showing signs of healing.

But this is also true: overall, native fish numbers at the Fishway have been declining steadily over the past 20 years. Since the peak years for native fish coming into the marsh between 2020 and 2004, by 2025 the number of all native fish species arriving at the fishway have declined by over 70%. This is not unique to Cootes Paradise. Other agencies have observed the same thing in Hamilton Harbour and across Lake Ontario’s shoreline. The health of the fish community is still below targets set for the Harbour’s recovery.

There are genuine winners too. White suckers, a native species, became the most abundant fish at the Fishway in 2025 with 3,977 coming in, over half of the total. Bowfin numbers have grown too, with six times the number of fish recorded in 2025 compared to 2000: tough, ancient fish that tolerate warm, low-oxygen water that would kill less adaptable species.

The reasons for the declines are not simple. Issues include excess nutrients from fertilizers and wastewater, warm oxygen-depleted water in summer, habitat recovering faster than its biological community can follow, novel chemical compounds washing off urban surfaces in ways we are only beginning to understand, and disease, which is difficult to study. The pressures extend out into Lake Ontario, where changes in prey fish populations may be reducing the food available to species all the way up the chain.

Fish populations also reflect everything fish experience during their migrations. Locally, Hamilton Conservation Authority has removed old dams on Spencer Creek to reopen ancient migration routes. Each year RBG manages creeks entering Cootes Paradise and Carrolls Bay to help fish reach their spawning grounds. We use innovations like Christmas Tree berms to direct sediment deposition away from channels. This is essentially restoration through bioengineering and shoreline plantings, improving fish habitat by encouraging creeks to develop habitat complexity, with shrubs that overhang to cool waters and provide refuge spots. Sediment deposition along banks allows native bulrushes and cattails to regrow.

RBG has been working for decades to improve the habitat arriving fish need to spawn. What we are seeing in Cootes Paradise is a wetland in early succession. The natural seed bank for a diverse native plant community lies buried under years of nutrient-rich sediment, in shallow, warm water. Every late summer, algal blooms roll in and undo some of the season’s gains.

What happens outside the the wetland is inseparable from what happens in it. How we manage lawns, stormwater, creek banks, and the harbour and lake matter, as they all connect. Backed by thirty years of careful, consistent Fishway data, we have an unusually clear window into the health of a significant coastal wetland and its connections to the broader lake ecosystem. That window is showing us something we should not look away from.

Everyone can help. The most important thing we can each do is minimize nutrients and runoff entering our waterways. Use fertilizer sparingly. Everything that goes onto the land eventually ends up in a wetland. Use native plants in your yard, since they support insect populations, and insects are what fish eat. Infiltrate rainwater where it falls rather than letting it race across pavement into storm drains and the lake. Small choices made by many can add up to huge benefits.

RBG is running weekend lifts at the Cootes Paradise Fishway for World Fish Migration Day on 23 May, at 10 a.m. and 2 p.m. Come out and see the Fishway in operation, promoting and recording native fish migrations and intercepting invasive species. Learn more at rbg.ca/fishway.

Aerial photo courtesy of Hamilton-Oshawa Port Authority.