Cyanobacteria has been found at Pirita beach in Tallinn and in Lake Peipsi, the Health Board confirmed this week. Bathers should monitor their health after swimming.
Water samples taken from Pirita Monday showed a small level of the toxic algae in the sea which points to a moderate bloom.
On Friday, the agency said Lake Peipsi and Kallaste in eastern Estonia are experiencing a similar situation.
A larger patch has been observable off Estonia's north coast for a week or so. Cyanobacteria blooms depend on water temperature and wind direction.
The Health Board recommends bathers pay attention to their health after swimming in the sea and wash with soap and water afterward. Children and pets should not be allowed to swallow seawater from shallow areas.
It is possible to be poisoned by the algae toxins and small children, the elderly and animals are particularly at risk. Symptoms include those similar to the flu along with reddening of the skin and eyes, diarrhea, fever, runny nose and cough, muscle aches and dizziness.
If poisoning is suspected, contact the Health Board's 24-hour hotline on 16662.
Editor: Helen Wright