Excerpt from
History of the Long Railroad Bridge Crossing Across the Potomac River
http://www.dcnrhs.org/learn/washington-d-c-railroad-history/history-of-the-long-bridge
With the outbreak of hostilities between North & South and Virginia's May 23, 1861 secession from the Union, the Long Bridge now took on a new, added importance.
Alexandria was quickly occupied by the Union Army and the US Military RR and the bridge's north and south shores were well guarded by Federal troops, ever vigilant for spies, infiltrators, contraband and of course, invasion. Let us remember that the White House, President Lincoln, the Capitol and the entire Federal Legislature were less than three miles from water's edge.
Rails were now placed on the ancient, rickety bridge. It was quickly confirmed that the structure could not safely support the weight of locomotives and freight cars. Instead, lightly loaded railroad cars were transhipped across the mile-long structure, pulled by good old-fashioned horse power.
Not until 1863 was a new, stronger, parallel structure completed, one which could hold the weight of newer, heavier locomotives and freight cars.
The lack of an adequate crossing during the first years of the war was a motivation, at least in part, for the US Military RR headquarters to be located in Alexandria. Of course, the 'ready-made shops' of the Orange & Alexandria and other railroads in that city had something to do with their decision, too.
This new bridge was constructed about 100' down river and had two draw spans like its parallel predecessor. Both structures remained in use throughout the remainder of the Civil War.