The Regulatory Reform (Scotland) Bill, currently at stage one in its journey through the Scottish Parliament, proposes to give the Scottish Environment Protection Agency additional powers to deal with businesses that do not comply with legislation.
If passed by parliament it could give the body the scope to issue fines of up to £40,000.
Business Stream, the water solutions company, warned the new regulations could signal the start of a clampdown on offending businesses.
Ian Hewson, head of water and waste water solutions, said: "Many of the businesses we work with do not know the full extent to which trade effluent regulations can impact on them, and £40,000 is a lot of money to pay for a problem that is so easily managed.
"Trade effluent is not often the kind of subject people like discussing, but getting it wrong can be damaging financially, operationally and could even cost a business its reputation."
As well as facing fines, Business Stream said firms that breach the rules could face enforcement action such as being forced to manually remove effluent.