A speculative study suggests that the loch was created by glacial deposits from the surrounding Ochil Hills at the end of the last ice-age.

The water level and shoreline have changed over time due to roads, railway, sluice gate and farmland.

Lindores Loch is a protected Site of Special Scientific Interest (SSSI) and is designated for the flora and fauna of its wetlands and open water habitats.

Specifically its high diversity of pondweeds (potamogeton), large area of reed bed, wet woodland and notable birds.

In 1617 armed vandals destroyed two mills belonging to Sir Michael Balfour of Denmilne by demolishing the dam.