 On May 31 , as McClellan planned an assault , his army was surprised by a Confederate attack . Johnston saw that the Union army was split in half by the rain @-@ swollen Chickahominy River and hoped to defeat it in detail at Seven Pines and Fair Oaks . McClellan was unable to command the army personally because of a recurrence of malarial fever , but his subordinates were able to repel the attacks . Nevertheless , McClellan received criticism from Washington for not counterattacking , which some believed could have opened the city of Richmond to capture . Johnston was wounded in the battle , and General Robert E. Lee assumed command of the Army of Northern Virginia . McClellan spent the next three weeks repositioning his troops and waiting for promised reinforcements , losing valuable time as Lee continued to strengthen Richmond 's defenses . 
