The Environment Department says 59 of the 65 samples taken last September and October had elevated fecal coliform bacteria counts.
Many samples also showed high nutrient levels, which can lead to algae blooms.
The tests were carried out by the Acadia Centre for Estuarine Research in the Annapolis, Cornwallis and Habitant rivers.
Environment Minister Randy Delorey says the report is a reminder coliform bacteria and other potential contaminants may be found in surface water open to elements such as weather, animal activity and malfunctioning septic systems.
Gary O'Toole, director of environmental health with the Health Department, says no increase in food or water-borne illness was found when the samples were taken.