Merrick is best known for his role in the case of Murphy v. Porter during the American Civil War. He was a federal judge on the U.S. Circuit Court for the District of Columbia in October 1861 when he issued a writ of habeas corpus to James Murphy. President Abraham Lincoln, who had suspended habeas corpus despite his actions being ruled unconstitutional in Ex parte Merryman, extended the suspension to the District of Columbia where the writ was refused. In retaliation for the writ, Lincoln ordered Merrick placed under house arrest to prevent the meeting of the Circuit Court panel to review Murphy's case.

The Circuit Court panel met anyway, absent Merrick, on October 19, 1861 and issued a contempt of court citation against General Andrew Porter, the Provost Marshal for the District of Columbia who commanded the soldiers holding Merrick under house arrest. President Lincoln again intervened blocking the Deputy United States Marshal from serving the contempt citation against Porter. The Circuit Court reconvened and ruled that Lincoln had "seen fit to arrest the process of this Court" in violation of the Constitution.

During the affair Lincoln also ordered Secretary of State William Seward to suspended Merrick's salary - an act that is also prohibited by the United States Constitution. Merrick was released from house arrest in December.

Merrick served as the Howard County representative to the 1867 Maryland Constitutional Convention. This followed the election of 1866 when the pro-Union politicians lost power and pro-slavery Democrats replaced them. They sought to rewrite the Constitution of 1864, which they believed to be pro-Union. The convention was called at the request of Governor Thomas Swann, a Democrat elected in 1866.

In 1870, he served as a Democrat in the Maryland House of Delegates representing Howard County. In 1871, he was sworn in to serve as a Democrat to Congress, serving the 5th Congressional District that included Anne Arundel, Calvert, Charles, Howard, Montgomery, Prince George's, St. Mary's and part of Baltimore County. All five of Maryland's Congressmen were Democrats. He only served one term and, after redistricting, was replaced by William J. Albert, a Republican.