Castle Cement Ltd admitted four charges relating to dust and noise nuisances at Padeswood as well as two fires which released potentially dangerous smoke.
The Environment Agency Wales (EAW) said the UK£300,000 (EUR345,000) in fines and costs was one of the highest ever court awards.
Despite the possible increased risk of cancer, and other illnesses, Mold Crown Court heard no cases had been detected.
The charges covered a period between August 2005 and May 2007.
The company also asked for a further offence bringing matters up to October 2009 - involving an escape of 250 tonnes of dust from a broken pipe - to be taken into consideration.
EAW said the fine and total costs were "one of the highest ever awarded for an environmental offence in the UK".
Judge John Rogers QC said it was accepted there was no evidence of actual harm to any members of the public.