The two promoted teams were replaced by FSV Frankfurt and Paderborn, who finished in the bottom two places of the 2015–16 2.
The three relegated teams were replaced by the three winners of the 2015–16 Regionalliga promotion playoffs.
Jahn Regensburg from the Regionalliga Bayern, immediately returned to national level.
Zwickau from the Regionalliga Nordost returned to third level after 16 years and will make their debut in 3.
Sportfreunde Lotte from the Regionalliga West is playing its debut season in the 3.