There are two primary types of contamination; biological, i.e. viruses and other pathogens or chemical, such as metals, dioxins and PCBs etc.
DFO routinely monitors the quality of shellfish, because they are filter feeders and can become readily contaminated with fecal coliform and other pathogens that can be passed onto humans. This is why many beeches are closed to shellfish harvesting around built up areas where there sewage or animal fecal matter (ducks/geese etc) is more likely to impact surface water quality. As noted by TimL, crab meat is generally safe to eat from a biological and chemical perspective, but the hepatopancrease may accumulate chemicals that if consumed frequently enough may pose a risk to human health.
I am not aware of any government agency that routinely monitors the quality of fish meat. The reason for this (I believe) is that water and food ingested by fish goes through their gut where it is digested and is then absorbed through the gut wall, which prevents the fish meat from becoming contaminated with biological agents. However, there is a potential risk that fish flesh can become contaminated with chemicals, if the habitat they live in is contaminated. The degree of impact to the flesh will be dependent on the nature of their food source, the degree of contamination in the environment and the age of the fish. The younger the fish the less contaminants accumulate within the fish.
I work in the environmental field and apart from some very site specific locations where significant environmental impacts are thought to be present, such as the Trail lead smelter or the recent Mount Polley mine site release, assessment of contamination in fish is not considered to be warranted. Some fish will also accumulate mercury from natural and man made sources. This can be an issue in some large marine fish such as Tuna, because the mercury levels can accumulate at significant levels. However, this is not an issue in shorter lived species such as salmon, where any minor risk of additional mercury consumption is far outweighed by the benefit of eating fish.
While shallow and warm urban lakes with a lot of wildlife may be polluted, that pollution is likely only from fecal matter, which is unlikely to adversely impact the fish flesh. As long as the guts are removed and the fish is rinsed well I doubt there would be any problem eating fish from these lakes.