I agree with Archimedes. Our muscles adapt and get pretty efficient at any exercise we do regularly. Your muscles are adapted to regular running, but when you switch to a new exercise, they are far less efficient, which is why you are getting fatigued in just a few minutes. If you continue to swim regularly, your muscles will adapt to this, and you will find swimming easier.
The other thing is that the arms are the main thing propelling you through the water, and there is a lot more arm effort in swimming than there is in running. These muscles may not have built up the endurance that your leg muscles have.
The other thing about swimming is breathing, and trying to find a breathing pattern that fits with your stroke. It is possible that you aren't breathing often/deep enough, and the lack of oxygen is what is holding you back.
The reasonable man adapts himself to the world; the unreasonable one persists in trying to adapt the world to himself. Therefore all progress depends on the unreasonable man.
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