In 1863, Welles relented and allowed Skerrett to be assigned to the screw sloop , which participated in the Union blockade of Wilmington, North Carolina, and in hunting Confederate States Navy ships raiding merchant shipping in the West Indies. He then transferred to the gunboat in the Western Gulf Squadron, which was enforcing the Union blockade of Confederate ports in Texas. Aboard "Aroostook", he finally saw action on 27 June 1864 during combat against Confederate forts at the mouth of the Brazos River in Texas. He served aboard "Aroostook" in Texas waters through the end of the war in 1865.