Daniel Kawczynski said that the Welsh Government's new laws on the spreading of manure could lead to slurry being dumped on the English side of the border, contaminating water supplies.
"Farmers who have land on both sides of the border will be banned from spreading slurry in Wales, so they will be bringing their slurry across the border into Shropshire," said Mr Kawczynski.
"Our concern is the huge amount will be poured into Shropshire's streams and rivers."
Mr Kawczynski said he would be writing to Environment Secretary George Eustice voicing his concerns about the implications of the new rules.
The Control of Agricultural Pollution Regulations, which come into effect on April 1, seek to reduce nitrate pollution. The rules will be phased in over a three-year period.
Mr Kawczynski said it was just another example of the Welsh administration causing problems in border communities by diverging from the rest of the UK.
"This has the potential for serious environmental damage as a result of artificial borders that are being imposed on us by separatist movements," he said.