To assess the ecological condition of aquatic ecosystems, water samples are collected three times annually (spring, summer and fall) from nine streams and rivers in the Park. This measure covers a watershed catchment area of greater than 50% of the total park area. Each sample includes water temperature, dissolved oxygen, pH, and conductivity collected in-situ (i.e. at each stream), and nutrients and metals obtained from samples analyzed by the National Laboratory for Environmental Testing (Environment and Climate Change Canada), as well as the water chemistry lab (Great Lakes Forestry Centre, Natural Resources Canada). With this data, each stream is assessed for acidification, eutrophication and metal loading, and the results are expressed as a single water quality index (WQI) per stream and for the Park. Scaled between 0 and 100, a WQI of greater-than-or-equal-to 80 is good.

In 2016, Pukaskwa had a WQI of 80.4 or ‘good’ ecological condition, a result that has been stable over the past five years. Despite the good assessment, exceedances of cadmium commonly occur. Cadmium is toxic to fish and invertebrates and the principal anthropogenic source is industrial effluents from refining and smelting (e.g. possibly from long range pollution). It is unknown however, if the source of cadmium in Pukaskwa National Park is anthropogenic or if levels are naturally elevated in this region.