Officers, drones and dogs descended on the farm in Skendleby, near the east coast, on the morning of Thursday 3 September.
The Spanish Civil Guard also joined the operation, having provided information which supported intelligence obtained by Lincolnshire Police that a drug operation was taking place.
Four bunkers comprised of a total of 12 shipping containers were found 20ft below barns, and within them officers unearthed an abundance of cannabis plants, with an estimated street value of £580,000 ($746,700).
Authorities spent a total of nine days searching the site, and on top of the huge drugs haul, they also discovered more than 300 tonnes of illegal waste, a shotgun and six stolen cars.
One llama and 22 horses were found in poor health and taken away.
Three men - aged 28, 34 and 35 - were arrested on suspicion of production of a Class B drug, burglary with intent to steal, animal welfare offences and possible waste offences.
The 34-year-old was also arrested on suspicion of possession of a prohibited firearm and theft of a motor vehicle.
They have been released on bail while the investigation continues.
Detective Superintendent Rick Hatton said: "We are extremely grateful to our counterparts in Spain and our partners for assisting with the exploration of this site.
"With the operation being underground we have needed some real specialist support to uncover this activity.
"Only with the skills of those who joined us from Lincolnshire Fire and Rescue, the Environment Agency, East Lindsey District Council, RSPCA, Dyno-Rod and the Home Office's Defence Science and Technology Laboratory have we been able to get to this point."
Seven Environment Agency officers who took part in the search found around 300 tonnes of baled waste, 60 part-dismantled vehicles, used asbestos roofing materials, household rubbish and mixed manufactured wood, plus evidence of six separate illegal burn areas.
Environment Agency Area Director Norman Robinson said: "Waste crime is serious.
"It blights communities and risks real harm to people's health and the environment, and we won't hesitate to take action against those responsible.
"We've now been able to put a stop to illegal activity on this site - a testament to the determination, joint-working and intelligence-sharing between multiple organisations.
"Investigations continue, but in the meantime, we'd ask anyone who suspects illegal waste activity to report it to our hotline on 0800 80 70 60 or anonymously to Crimestoppers on 0800 555 111."
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