 The lack of decisive action on the Virginia Peninsula spurred President Abraham Lincoln to order McClellan 's army to move into positions close to Richmond . By May 30 , McClellan had begun moving troops across the Chickahominy River , the only major natural barrier that separated his army from Richmond . However , heavy rains and thunderstorms on the night of May 30 caused the water level to swell , washing away two bridges and splitting the Federal army in two across the Chickahominy . In the subsequent Battle of Seven Pines , Confederate general @-@ in @-@ chief Joseph E. Johnston sought to capitalize on the bifurcation of McClellan 's army , attacking the half of the Union Army that was stuck south of the river . Johnston 's plan fell apart , and McClellan lost no ground . Late in the battle , Johnston was hit in the right shoulder by a bullet and in the chest by a shell fragment ; his command went to Maj. Gen. Gustavus W. Smith . Smith 's tenure as commander of the Army of Northern Virginia was short . On June 1 , after an unsuccessful attack on Union forces , Jefferson Davis , the President of the Confederacy , appointed Robert E. Lee , his own military adviser , to replace Smith as the commander @-@ in @-@ chief of the Confederate armies . 
