Cramer said he first discussed the rule -- which would redefine which streams, rivers and wetlands receive automatic protection under the Clean Water Act -- with Trump at a town hall meeting in Iowa.
If he were to advise Trump as president, Cramer said, he would suggest that he "tackle the Clean Water Act itself" rather than simply address the question of which waters fall under the scope of the law.
"[Let's] bring more clarity and specificity, more prescription to [the Clean Water Act], as well as the Clean Air Act and other broad authorities that have provided this opportunity for this type of mischief by administrations, be they Republican or be they Democrat," he said.
EPA and the Army Corps began the rulemaking process in 2014 to standardize which waters were protected as "waters of the United States."
Two Supreme Court decisions in 2001 and 2006 muddled the definition. As a result, determinations of which waters fell under federal jurisdiction were made on a case-by-case basis, leaving certain water bodies vulnerable to unregulated pollution.
The rulemaking was fiercely criticized by developers and agricultural organizations, which viewed the regulation as an expansion of federal control over private landowners. Dozens of lawsuits were filed after the rule was finalized last year. The regulation is currently stayed in federal court pending the outcome of the litigation.
It's likely that the courts won't decide the rule's fate until after President Obama leaves office.
Cramer said he would expect the statutes to be rolled back in the first 100 days of a Trump administration, or over the two-year course of a Republican-held Congress.