Dust storms on Mars play a role in transporting water from its lower to upper atmosphere, seasonally enhancing hydrogen escape. However, it remains unclear how water is diurnally transported during a dust storm and how its elements, hydrogen and oxygen, are subsequently influenced in the upper atmosphere. Here, we use multi-spacecraft and space telescope observations obtained during a major dust storm in Mars Year 33 to show that hydrogen abundance in the upper atmosphere gradually increases because of water supply above an altitude of 60 km, while oxygen abundance temporarily decreases via water ice absorption, catalytic loss, or downward transportation. Additionally, atmospheric waves modulate dust and water transportations, causing alternate oscillations of hydrogen and oxygen abundances in the upper atmosphere. If dust- and wave-driven couplings of the Martian lower and upper atmospheres are common in dust storms, with increasing escape of hydrogen, oxygen will less efficiently escape from the upper atmosphere, leading to a more oxidized atmosphere. These findings provide insights regarding Mars’ water loss history and its redox state, which are crucial for understanding the Martian habitable environment.