The application, from Patersons of Greenoakhill, was rejected by the council's planning committee on Tuesday morning following a lengthy protest campaign by locals.
If permission had been granted, 4.6 million tonnes of sand and gravel would have been extracted over a period of between 11 and 15 years.
In the report, planning officials stated that insufficent information had been submitted to assess the potential environmental impact as well as concerns regarding the effectiveness of a 20 metre flooding 'buffer zone' between the quarry and the River Clyde.
Local councillors Bev Gauld and Hamish Stewart also threw their weight behind the campaign during the meeting itself.
The campaign against the quarry began last year when residents from Biggar, Lamington, Coulter and other surrounding villages formed the Clyde River Action Group (CRAG).
As well as enviornmental concerns the group, led by chairwoman Caroline Parker, believed that the number of lorries serving the quarry going through the villages would be disastrous and that tourism would also suffer.
For more information on this article, see this week's Lanark Gazette which is in the shops now.