A well plate assembly includes a well plate with a base wall, a peripheral wall extending up from the base wall and spaced inwardly from the outer periphery of the base wall. A well array is formed on the base wall at locations inwardly from the peripheral wall. A lid is mounted on the peripheral wall of the well plate. The lid and the peripheral wall have areas that are indented from the outer periphery of the base wall to facilitate manipulation by robotic stacking equipment. The well plate and the lid further include substantially registered robotic gripper plates aligned with the outer periphery of the base wall to facilitate manipulation of the assembled well plate and lid by robotic grippers.