The Waves have compiled a 36-hole total of four-over par 572 heading into Friday's third round.
Action at the four-day tournament continues through Saturday.
Pepperdine posted a four-over par total of 288 today after completing the rain-suspended first round earlier in the morning with an even-par score of 284.
The Waves bolted out to a fast start in the second round, and actually held the lead in the team standings for a period of time after reaching an eight-under par total at one juncture.
Clemson and Georgia Tech hold the lead in the team standings with a five-under par score of 563, one stroke ahead of Toledo. North Carolina, Texas and Texas Christian are each tied for fourth place with two-under par totals of 566.
Brock Mackenzie of Washington holds the lead in the individual standings with a seven-under par score of 135 after firing rounds of 66 and 69.
Dustin Bray of North Carolina and Adam Rubinson of Texas Christian are tied for second place with six-under par totals of 136.
Pepperdine is paced by the freshmen tandem of Brian O'Flaherty and Michael Putnam. Both are among a group of 12 players tied for 23rd place at one-under par 141.