Until Samus has the Gravity Suit, it is very difficult to move underwater without tons of slowdown. You can circumvent this by repeatedly using the spin jump to go slightly faster. Alternatively, you can be in Morph Ball form and use the Spring Ball to jump forward as well, but the spin jump has more forward momentum. Once you have the Speed Booster, you can even Shinespark underwater without the Gravity Suit as long as the Shinepark is stored prior to touching the water.
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