Suppose you hold your breath and dive a meter underwater. Assuming the surface area of the back of your body is approximately $1$ m$^2$, you have about $1$ tonne of weight above you. If you were out of the water and someone put a 1 tonne rock on your back, I think you would die. How are you able to survive underwater?
Materials (including your fragile body) are far more robust against uniform triaxial compressive stress (also known as hydrostatic stress, also known as pressure) than against other stress configurations (search for "submarine hulls" here). The atoms move imperceptibly closer, but this isn't hazardous, in contrast to the shear or tensile tearing/cracking that can arise in biological tissues from unbalanced stress states.
The pressures you'd encounter underwater during diving have essentially no mechanical effect on condensed matter (solids and liquids), aside from compressing your lungs and the air within.
Atmospheric air pressure is 15 psi. That translates to a total force over 1 square meter of your body of about 11.5 tons. And we’re not crushed by it. The reason is the internal pressure caused by our bodily fluids and tissues balances the external pressure. Our bodies are more than able to handle a 10 % increase in external pressure from being submersed under 1 meter of water.
Hope this helps.