The Trump Organisation has submitted plans for a second 18-hole course at the Menie resort.
If given the go-ahead, the course would be named Mary Macleod after Mr Trump's Scottish mother.
Sepa wants the plans to be revised over sewage and pollution concerns.
The Trump Organisation already owns an 18-hole course at the site.
Aberdeenshire Council is due to discuss the planning application at a meeting on the 22 August.
In its submission, Sepa detailed concerns over waste water drainage associated with the planning application.
The environment organisation also raised concerns about proposals to plant non-native plants near Hole 5 of the course as well as a failure to supply an up-to-date environmental management plan.
A spokesperson Sepa said: "As a statutory consultee under planning regulations, Sepa has noted a number of objections to the current proposals in relation to provision of waste water disposal and wider protection of the water environment.
"If further information or revised proposals are presented by the Trump International Golf Links that alleviate these concerns, Sepa would consider removing our objections."
The Trump Organisation will now have the opportunity to revise its plans to comply with Sepa's demands.
Trump International Golf Links said in a statement: "The recent correspondence between Trump International, the local authority and statutory consultants is a normal part of the planning process and the regular ongoing dialogue conducted during the application process.
"SNH and Sepa always reference a range of policy considerations and factors which is standard practice and nothing out of the ordinary.
"Our application is making its way through the planning system and this dialogue will continue until it goes before committee for consideration.
"The Dr Martin Hawtree designed second golf course is located to the south of the Trump estate and does not occupy a Site of Special Scientific Interest therefore is not covered by any environmental designations.
"We are extremely confident in our proposal and that this process will reach a satisfactory conclusion acceptable to all parties on our world class development."
The Scottish Environment Protection Agency (Sepa) has raised formal concerns to Donald Trump's company's proposals for a new golf course in Aberdeenshire.