A report from the Canadian Nature Federation describes these as "critical threats".
Some areas are being hit hard by industry, particularly logging and cranberry farming and processing.
Others are affected by virtually unchecked poaching of species such as eider ducks.
Many landscapes are also becoming home to non-indigenous species of plants and sea-life, damaging the habitats needed for local species to survive.
Too little money
It is claimed, for example, that the arrival of zebra mussels has wrecked the ecological balance of some areas of the great lakes, and helped pass dangerous PCB chemicals up the food chain into waterfowl.
In addition, a recent WWF report suggests that the low arctic tundra which makes up much of northern Canada will be among the areas worst hit by predicted climate change.
There are 49 National Wildlife Areas, and 94 migratory bird sanctuaries in Canada, occupying an area equivalent to the province of Nova Scotia.
All of these have a combined annual budget of only $1.7m, and the report says that this is far too little to counter the threats they face.
Volunteer decline
The report says: "The current lack of capacity and resources within the Canadian Wildlife Service is seriously impeding its ability to protect this network effectively.
"Most sites are not actively being managed, enforcement activity is sporadic, there are significant public and employee health and safety liabilities and the ecological integrity of many sites is at risk."
The whole system is in "jeopardy", it says. "Non-government research links are being lost, volunteers are declining.
"On-site buildings, roads and trails are left in degraded and often dangerous condition."
Better staffing
Julie Gelfand, the president of the Canadian Nature Federation, said that far too little money was being spent on Canadian wildlife areas.
She said: "It's just 15 cents a hectare. In contrast, the US spends more than $12 a hectare on wildlife refuges.
"This report outlines a series of recommendations to ensure the health of wildlife areas, upon which Canada's species at risk and migratory birds depend for survival."
The recommendations include increases in the number of on-site staff to discourage poaching as well as carrying out vital research and maintenance.
The report also calls for changes to the boundaries of wildlife areas to stop encroachment by urban expansion into vulnerable habitats.
And it is calling for an increase in the number of national wildlife areas from 49 to 100 by the year 2006.