As reader Will Keene pointed out, the OR holds some clues as to the position of Matamoros in the ACW.
March 1, 1862. . L. Pierce, Jr. establishes himself as U.S. consul in Matamoros, notifying Seward that the Confederates used "every possible exertion to get me driven out." He says they control both banks of the Rio Grande at its mouth and that there is only one U.S. ship in port to carry his message out. He notes that "Matamoros is now the great thoroughfare to the Southern states."
March 21, 1862. Pierce notifies Seward that he is "besieged" by Union refugees and deserters from the Confederacy and lacks the means to send them on to the North. He is finding "subsistence" for them to the best of his ability.
March 24, 1862. We find Consul Pierce telling Seward that the local Mexican colonel commanding has told Pierce that Texas was organizing a cross-border raid to seize Matamoros in order to arrest Union men operating there - including the consul himself. He makes this interesting comment: "The Texan troops are becoming demoralized and disorderly in the extreme…" I assume this refers to the troops that would later be formed into the Fist Texas Cavalry U.S.
April 25, 1862. Seward tells Stanton of a British ship with contraband changing destination from Charleston to Tampico. He says that since Tampico cannot be blockaded, the War Department needs to put a force into Brownsville and on the Rio Grande.
May 5, 1862. Pierce tells Seward of an employee abducted by four Texas Rangers in Mexico and taken to Fort Brown, an English subject. On demands for his release, the Texans let him go but retain the official correspondence he was carrying. Pierce notes "the crowds of refugees from texas do not diminish in the least."
May 23, 1862. C.B. H. Blood, U.S. consul in Monterrey writes Seward to say a small group of Mexicans is feeding and sheltering refugees spilling across the Texas border and that there is no U.S. provision for these people; he asks for instructions or advice. He is currently turning American citizens into the street, he says, to seek a living among an already destitute population. He estimates 300 Americans are being fed by charity in Monterey and expects 3,000 Texans would enlist under U.S. colors in the border area. He reports of the hanging of four Texas Home Guards who sought to desert to a U.S. steamer. In closing he asks that if the government will not feed the refugees that collections be made in U.S. cities for them.
That is all I found.
There is one Confederate message referring to the city.
April 27, 1864. Rebel Gen. John Magruder writes to John Slidell, commissioner to France, to report 10 pieces of federal artillery being donated to Mexico and the Mexican provincial governor walking arm-in-arm with the "pretended governor of Texas" John Hamilton. He refers to the federals "wantonly" and "openly" supplying arms for the carrying out of the war (in Mexico) against France.
Don't think we exhausted the topic, though...