Walker gets $3.3 million and McDonald $3,025,000 in deals that were completed Thursday.
Walker hit .280 with 14 home runs and 69 RBIs in 129 games last season but missed significant time due to a back injury. The 27-year-old Pittsburgh native made $500,000 in 2012 and was arbitration-eligible for the first time this winter. He asked for $3.6 million and was offered $3 million by the Pirates.
The 28-year-old McDonald, who made $502,500 last year, went 12-8 with a 4.21 ERA but struggled for most of the second half. He requested $3.4 million in arbitration while Pittsburgh countered at $2.65 million.
McDonald is expected to be the team's third starter in 2013 behind A.J. Burnett and Wandy Rodriguez.
The deals mean the Pirates have reached agreement with all their arbitration-eligible players. Pitchers and catchers report to camp in Bradenton, Fla., on Feb. 11.