Johnny is disadvantaged by still thinking vertically, not to mention the whole needing to breathe regularly thing. Zagreus, by dint of physiology and better control of dreams and fear, isn't even really trying to stay afloat in the first place. Johnny's blows are strengthless, easily ignored, and Zagreus claws at Johnny's shirt, tangling their legs, keeping Johnny from treading water or kicking off. He fights like something that belongs in dark water, weighing Johnny down, a constant insinuation, slinging an arm around his neck when he reaches for the boat. Johnny wanted him in the water, so in the water they both stay.