The Union Army that attacked the Confederates at Manassas in July, 1861 was green. Lincoln told his commander to attack anyway, since the Confederates were equally untrained. McDowell's forces were successful at pushing Bureauregard's forces off Mathews and Buck Hill, and appeared to be able to march to the railroad junction.
However, McDowell took too long to organize his forces and then attacked regiment by regiment, rather than with larger units. Confederate reinforcements arrived on the Manassas Gap Railroad, and the Confederate generals were effective internoon, getting them into battle. In the late afternoon on July 21, 1861, the Federal forces on Chinn Ridge started to retreat, and by the time the sun had set the Union Army was in a chaotic retreat to Alexandria.
The Confederates were as disorganized by victory as the Federals were by defeat, so there was no pursuit east of Centreville. Both sides spent the rest of 1861 organizing more troops than had had ever been assembled in any previous American army, and fighting was minimal. Fighting in the winter of 1861-62 was unrealistic for another reason - horses provided the primary transportation for hauling military supplies and artillery, and the horses needed grass in pastures to "refuel." An army marches on its stomach. In the winter, when pasture grass was scarce and hay for horses was difficult to haul, an army in the Civil War could not march far.
By October, 1861, the Confederate politicians and generals were in public disagreement as they tried to assign the blame for the lost opportunity to seize Washington after First Manassas. At that time, the Confederates had outposts on Munson and Union hills in Arlington, and forces based at Fairfax Courthouse. They even placed enough cannon on the Virginia shoreline to block ships from sailing past modern-day Leesylvania State Park, cutting the river supply line and forcing the Union Army to get most of its supplies via one rail line connecting Washington with Baltimore.

The logistics of supplying the Confederate front lines grew worse with wet weather in October, so they withdrew to Centreville. In the winter, however, even Centreville was a long wagon haul from Manassas Junction. The Confederates built the first military railroad in November 1861-February, 1862 to cross Bull Run and climb the hill. Ultimately, the Centreville Military Railroad reached what today is a McDonalds on Route 28, south of the modern junction with Route 29.
The Virginia Central, Orange and Alexandria, and Manassas Gap railroads brought supplies and troops to Manassas Junction, after they were initially stationed at other locations in Virginia until they were "seasoned," or past the stage when soldiers from isolated rural areas in the South were likely to become disabled by their first exposure to communicable diseases such measles. Confederate encampments were scattered along Bull Run, from Occoquan upstream to Centreville and the modern location of the Manassas campus of Northern Virginia Community College. (Modern relic hunters know that encampments are likely locations for valuable buttons, belt buckles, bullets, etc. Battlefields were occupied for only 1 day, typically, but far more equipment was discarded at encampments that were occupied for months.)
Behind the lines, warehouses were built at Manassas Junction. Chapman (Beverly) Mill in Thoroughfare Gap, at the border of Prince Willias and Fauquier counties, also served as a supply depot. Over 1 million pounds of meat were stored there in the winter of 1861-62 to feed the Confederate Army.
The Confederate defense line along Bull Run appeared too strong to the General George McClellan, the Federal officer charged with the responsibility of capturing Richmond after Irvin McDowell had failed in July, 1861. McClellan identified another route to Richmond that would bypass the Bull Run defenses - sail the Union Army down the Potomac River to Fortress Monroe, then march up the Peninsula past Williamsburg to Richmond.
The Confederate response was to abandon Northern Virginia and to concentrate their forces near Richmond. The cannon in Centreville forts and along Bull Run were withdrawn. In some cases "Quaker guns" were substituted to disguise the reduced capabilities of the Confederate defenses. Troops were withdrawn quickly with little advance planning; the general staff of the Confederacy was small and unable to cope with the challenge. The Confederate railroad system was unable to carry the supplies as well as the troops to Richmond. The extraordinary Confederate effort to stockpile supplies since First Manassas required a massive destruction effort to prevent those same supplies from being useful to the Yankees.
