[1] He commanded the USS Lawrence in the Home Squadron as tensions escalated in the Gulf of Mexico prior to the Mexican-American War.

He and his crew spent the next year cruising along the Gulf Coast, providing security to American shipping in the region and helping suppress piracy.

[1] On 16 May 1861 Mercer took command of the newly recommissioned USS Wabash as the flagship of the Atlantic Blockading Squadron under rear admiral Silas H. Stringham.

Under Mercer's command, the Wabash captured the brigantine Sarah Starr in the waters near Charleston, South Carolina on August 3, 1861.

[6] Mercer was relieved from active command due to age, and served on the Navy Retiring Board until his death in Philadelphia on March 6, 1862.