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I finished reclaiming the divine beasts, and I decided to do some side quests. One of them requires me to defeat the Molduga in the Gerudo desert east of Gerudo Town, but I have no idea how to damage or defeat the Molduga to complete the quest.

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Bombs are your friend.

The Molduga detect movement on the sand, so this is the primary mechanic in dealing with them. In each of the Molduga areas, there are rocks or debris that you can use as a safe point. When you stand on the these, the Molduga will not be able to detect you.

From here, you can throw a bomb onto the sand, and when the Molduga gets close, it will notice the movement of the bomb. At this point, it will move toward the bomb, then jump out to attack. When it does this, you can trigger the bomb to stun the Molduga.

This gives you a window to run in and attack it at will. It will recover, so you can run back to safety, and repeat the process.

Of course, this is a basic method of how to deal with this, there are other methods you can invent to make things more interesting (like bomb arrows for example)

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    Bombs are your friend. -> Molduga vs Cuckoos – Wondercricket Nov 20 at 13:23
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    Cuckoos are clearly another perfectly viable and creative solution. – Ben Nov 20 at 14:42
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If you've already reclaimed Vah Naboris (Gerudo's divine beast), then by far the easiest way to defeat the Molduga is to just use Urbosa's Fury.

The 3 Urbosa's Fury shots you have are enough to kill the Molduga even without dealing any other damage.

And each Urbosa's Fury shot disables the enemy for a while, so you should be able to kill it in just 1-2 shots.

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