David Richard Thomas, of Bryndraenog Farm, pleaded guilty to failing to stop his cattle polluting a water course that is home to a rare type of mussel.
The River Clun is among the few remaining breeding grounds of the endangered fresh water pearl mussel, and a protected habitat.
But Thomas had allowed cattle access to the banks of the River Unk, which feeds into the Clun, which resulted in "polluting matter" that could harm the mussels entering the water course, Telford Magistrates Court heard on Wednesday.
Thomas had declined an offer to fund fencing that would stop the cattle getting access, and failed to act on a notice from the Environment Agency, served on January 20, to take action and install fencing on his land at Dutlas, on the Shropshire border with Powys.
He was ordered to pay a £13,000 fine, plus £1,000 in costs and £120 victim surcharge.
A spokeswoman for the Environment Agency, said: "Freshwater pearl mussels are in serious decline and River Clun is one of the few remaining sites where they can be found. Failure to act to protect them could result in proceedings from the European Union.
"When Mr Thomas failed to install the fencing, Natural England and the Environment Agency offered to fund the work. Unfortunately, this offer was declined so the Environment Agency had no alternative but to serve Mr Thomas with a notice to carry out the work."
The action comes as Shropshire Hills AONB Partnership has secured over £360,000 from the Wren Biodiversity Action Fund, Woodland Trust and Severn Rivers Trust to work with landowners to improve the condition of the River Clun Special Area of Conservation, a project which includes creating recovery sites for freshwater pearl mussels, which could die out in the next 20 years, it is feared.