This study aimed to measure muscle activity and motion kinematics during chair-based exercises under submerged and non-submerged conditions. Twelve healthy men performed chair-based standing and sitting movements. Surface electrodes were attached at the tibialis anterior, gastrocnemius, rectus femoris, biceps femoris, rectus abdominis, and erector spinae. The ankle, knee, and hip joint angles and forward inclination angle of the trunk segment in the sagittal plane were calculated. The mean muscle activities during both movements in the submerged condition for the entire motion were lower than those in the non-submerged condition except in the tibialis anterior and biceps femoris during the sitting movement (in the standing exercise, rectus femoris: 14.1% and 5.2%; and erector spinae: 18.3% and 13.6% in non-submerged and submerged conditions, respectively; and in the sitting exercise, rectus femoris: 12.1% and 4.5% and erector spinae: 12.9% and 9.9% in the non-submerged and submerged conditions, respectively). However, the integrated muscle activity in submerged conditions was similar or higher to that in non-submerged conditions during both movements, except for the rectus femoris. This was mainly due to the increased duration of motion (44.3% and 39.9% longer for standing and sitting exercises in submerged conditions, respectively, compared with non-submerged conditions; p < 0.01 for both). The hip joint flexion at the beginning and end of movement and forward inclination angles of the trunk segment at the beginning of the movement in the submerged condition were larger than those in the non-submerged condition during both movements (hip: 126.1° and 111.5° at the beginning, 182.3° and 178.4° at the end and trunk: 2.7° and 17.4° at the beginning in non-submerged and submerged conditions for the standing exercise, respectively; hip: 182.4° and 178.0° at the beginning, 125.9° and 111.1° at the end and trunk: 2.2° and 16.9° at the end in non-submerged and submerged conditions for the sitting exercise, respectively). Reduced or similar muscle activity but similar or higher muscular effort was observed in the submerged condition for all the muscles except the rectus femoris, with the upper body inclined forward. These findings could have beneficial implications for the prescription of exercise and rehabilitation regimens.