The regional government of Andalusia was seeking 89 million euros ($98 million) in compensation from the firm over the spill, which contaminated a vast stretch of rivers and wetlands with heavy metals including arsenic and mercury.
The catastrophe occurred when a wastewater reserve pool burst at Boliden's Los Frailes lead and zinc mine in the city of Aznalcollar, spewing more than five million cubic metres (17.5 million cubic feet) of highly acid sludge into the river and groundwater.
The toxic spill on April 25, 1998, killed tens of tonnes of fish and polluted nearly 5,000 hectares of fragile wetland.
The Andalusian government argued the 89 million euros was equivalent to the sums it spent to try to clean up the 4,643 hectares that were contaminated.
But a court in the southern city of Seville ruled that Boliden was under "no obligation" to rehabilitate the site.
Boliden has always denied responsibility for the disaster and blamed a subsidiary of Spanish construction company Dragados that built the wastewater pool.
"The decision of the court confirms our view that the extensive clean-up efforts that Boliden carried out and the compensation at the time of the accident were satisfactory," Boliden chief executive Mikael Staffas said.
The ecological disaster at the mine was one of the worst Spain has ever endured.
The government in Andalusia, where Aznalcollar is located, launched a civil suit against Boliden in 2002 after the dismissal of criminal cases brought by Andalusia, the Spanish state and environmental federations including Ecologists in Action.
The procedure was bogged down for years while Boliden launched repeated appeals, but in 2012 the Supreme Court ruled that the case against the company should go ahead.
Boliden was fined more than 45 million euros by the government in Madrid in August 2002 but it refused to pay on the grounds that it had not been found guilty in court.
The Aznalcollar mine, dropped by Boliden in 2001, is scheduled to reopen shortly, once new operator Mexican mining conglomerate Grupo Mexico obtains the outstanding authorisations from the regional authorities.
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