The Waterton Lakes Chain, over 100 kilometres of rivers and streams, wetlands, and about 80 lakes and ponds are all part of the park's living waters and ultimately the living landscape of the Crown of the Continent ecosystem.

While Waterton has relatively fewer lakes and ponds than other mountain national parks, it has more different types of waters and a wider variety of species living in them.

Abundant rain and snowmelt east of the continental divide flow through the park's two main watersheds, eventually flowing out via the Waterton River or the Belly River across the plains, through the boreal forests and into Hudson's Bay.

The park's mountain waters are cold (normally well below 15°C), high in oxygen and low in nutrients with little plant life. Although the abundance is low, the variety of life is high, with numerous kinds of bacteria, fungi, protozoa, insect larvae, snails, worms, planktons, plants, 5 amphibians and 22 fish.

Angling is a popular activity which can affect aquatic life. Knowing the unique and delicate balance within its aquatic ecosystems, the park must carefully manage this activity. The park has committed to allowing angling to continue as part of an overall recreational park experience. Fishing and some angling practices are not permitted when and where they damage aquatic ecosystems in the park.

New fishing regulations are shifting the emphasis to catching non-native species like rainbow, brown and eastern brook trout. This is part of the park's goal to restore healthy waters which have been affected by a history of fish stocking; a practice no longer considered appropriate in national parks. Native species are being restored and protected by regulation changes that will reduce hooking injury and deaths, and by protecting vulnerable spawning, migration and rearing areas.

Alberta's provincial fish, the bull trout, has declined throughout much of its former range in the province. Waterton is actively involved in the conservation of bull trout through ongoing management and research. Lake trout and the northern pike are also key species that indicate the health of living things in and on the water.

The Waterton Lakes Chain - Upper, Middle and Lower Waterton Lakes and the Maskinonge - is one of the most distinguishing and dominant features of the park. Together, these lakes make up almost two thirds of the total water surface area in the park.

They empty into the Waterton River, which drains a large area in both Waterton Lakes and Glacier (USA) national parks. As well, the international boundary runs across the Upper Waterton Lake about halfway down its length. For these reasons, the Upper Waterton Lake is the classic symbol of the Waterton-Glacier International Peace Park.

An often overlooked element of the park's vegetation and living waters are the areas that are a mixture of the two - wetlands. These intriguing places integrate much of what makes Waterton special - clear, clean waters, colourful and abundant plant life and a rich gathering of birds, invertebrates, herptiles and mammals. Wetlands are found throughout the park, but the largest and most notable is the Maskinonge, easily seen as you drive into the park.