St . Louis in the American Civil War St . Louis , Missouri was a strategic location during the American Civil War , an important city to the Union army and navy . It was a major supply depot and launching point for campaigns in the Western Theater . German Americans . Located near the junction of the Missouri River , the Illinois River and the Mississippi River , St . Louis was a major port and commercial center with a growing industrial base . The population reached 160 , 000 in 1860 and consisted mostly of Catholic German Americans and Irish Americans . The early Union volunteer regiments in St . Louis were mostly made up of the dominant German immigrants . St . Louis Arsenal . In March 1861 , Captain Nathaniel Lyon arrived in St . Louis in command of Company B of the 2nd U . S . Infantry . At the time the state of Missouri was relatively neutral in the dispute between North and South , but Missouri Governor Claiborne F . Jackson was a strong Southern sympathizer . Lyon was concerned that Jackson meant to seize the federal arsenal in St . Louis if the state seceded and that the Union had insufficient defensive forces to prevent the seizure . He attempted to strengthen the defenses , but came into opposition from his superiors , including Brig . Gen . William S . Harney of the Department of the West . Lyon employed his friendship with Francis P . Blair , Jr . , to have himself named commander of the arsenal . When the Civil War broke out and President Abraham Lincoln called for troops to put down the Confederacy , Missouri was asked to supply four regiments . Governor Jackson refused the request and ordered the Missouri militia to muster outside St . Louis under the stated purpose of training for home defense . Lyon allegedly disguised himself as a farm woman to spy on the militia camp and confirmed the presence of artillery stolen from a Federal arsenal . Lyon himself had been extensively involved in the St . Louis Wide Awakes , a pro - Union paramilitary organization that he intended to arm from the arsenal and muster into the ranks of the federal army . Upon obtaining command of the arsenal , Lyon armed the Wide Awake units under guise of night . Lyon had most of the weapons in the arsenal secretly moved to Illinois and on May 10 he led the 2nd U . S . Infantry to the camp , forcing its surrender . Riots broke out in St . Louis after Lyon marched his prisoners through the city . The event provoked the Camp Jackson Affair of May 10 , 1861 , in which Lyons ' troops opened fire on a crowd of civilians injuring at least 90 and killing 28 . The Camp Jackson Affair polarized the population of Missouri , leading many once - neutral citizens to advocate secession and setting the stage for sustained violence between the opposing factions . Civil War . During the Civil War , St . Louis stayed under Union control because of the strong military base , and the public support from loyal Germans . The largest percentage of volunteers served in the Union army ; some went south to fight for the Confederacy . Some people who stayed in the city during the war and supported the South smuggled supplies , medicine , and otherwise assisted Confederate soldiers . No major battles were fought in or near the city , but the Mississippi River was a vital highway during the war . Divided loyalties to the Union and Confederacy caused rifts in some families in St . Louis . Refugees . Thousands of black refugees poured into St . Louis , where the Freedmen ' s Relief Society , the Ladies Union Aid Society , the Western Sanitary Commission , and the American Missionary Association ( AMA ) set up schools for their children . St . Louis Riot . The division of loyalties between Union and Confederacy did result in loss of life on May 11 , 1861 . Union soldiers , the Fifth Regiment , United States Reserve Corps , Missouri Volunteers was attacked by a mob of Confederate sympathizers within hours of it being mustered into service . The regiment was marching from the Arsenal when the mob attacked it on the corner of Walnut and Broadway . Shots were exchanged and six persons were killed . The Fifth Regiment consisted primarily of loyal Germans , having been recruited primarily from men of the Tenth Ward of St . Louis .