Environmental Health has received notification from SEPA that there is blue green algae in the Lunnister Loch, Sullom and Spiggie Loch, Dunrossness.
Blue-green algae has also been found in Tingwall Loch, which runs into Asta Loch and Clickimin Loch.
The council says notices will be posted next to the lochs warning that contact with algal scum should be avoided.
Adjoining landowners have been advised of the situation, as well as anglers association, RSPB, as have NHS Shetland.
At this stage, the SIC says there is no adverse effect on water supplies.