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When you throw a rock on a lake it makes circular visible waves. Can it be that the rock causes a “expansive bubble” underwater that we can only see its borders on the surface?

Like the bubble made of the impact from Matrix Revolution fight scene.

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No, these are surface gravity waves. The magnitude of the motion decays exponentially with depth, $y$, into the water as $exp(-2\pi y/\lambda)$ where $\lambda$ is the wavelength.
In contrast, semicircular traveling vortices can be created that have properties somewhat along the lines you are thinking.

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    $\begingroup$ By comparison, an underwater explosion can cause a spherical shock wave, tho' again funny things happen when a portion of that wave reaches the surface . $\endgroup$ – Carl Witthoft Jan 12 at 13:13
  • $\begingroup$ @ Carl Witthoft Good point. Even just throwing a stone in, there will be accoustic compression waves that expands spherically at 340 m/s in the air and 1481 m/s in the water. I supose these must both create some tiny vertical displacements where they intersect the surface. $\endgroup$ – Roger Wood Jan 12 at 21:13

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