Nova Scotia's salmon rivers are generally short, rather than being part of long, and are without the complex watersheds found in many New Brunswick river systems.

Particular issues overshadow Nova Scotia salmon rivers. No other region, not even Lake Ontario and the upper part of the St.Lawrence River, where all its original salmon rivers lost their salmon, can match the 52 rivers in Nova Scotia whose salmon stocks were extirpated, mainly due to acid rain, an environmentally negative factor unique to Nova Scotia. Only three of of Nova Scotia's salmon rivers have been restored.

In the Inner Bay of Fundy many rivers have been declared endangered, and surveys have shown wild Atlantic salmon have entirely disappeared from some of these. As for New Brunswick's Inner Bay of Fundy runs, these salmon do not stray far beyond the Bay of Fundy instead of migrating long distances to Labrador or Greenland waters as do Outer Bay of Fundy salmon.

Salmon runs in the north of the province, in rivers exiting to the Gulf of St. Lawrence, are generally healthy, examples being the Margaree in Cape Breton, and River Philip on the mainland, not far from the NB border.