If you see "twinkling" with a light source that is much broader than the size of a possible particle or bubble in the beam (like a flashlight), then that implies something that is changing during the time the object is in the beam, and the only thing I can think of that changes in that way would be scattering from a nonspherical object (hence not likely a bubble) that is rotating/tumbling. In some orientations it will scatter more light than others and might cause "twinkling".
Along these lines, folks have shown that fluid flow can actually align microbes in the ocean, impacting light scattering by bacteria and phytoplankton:
Microbial alignment in flow changes ocean light climate
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3054027/
"Sunlight attenuates as it passes through seawater, exerting a fundamental control on marine productivity by limiting the depth at which photosynthesis can occur (
1–
3). The extinction of sunlight is governed by the inherent optical properties (IOPs) of seawater, which are determined largely by the light-scattering characteristics of suspended living and nonliving microscopic particles (
4)"
"Analogous to the shaken test tubes, the ocean can be characterized by intense fluid motion and abundant microorganisms. We demonstrate that the swirl patterns arise when elongated microorganisms align preferentially in the direction of fluid flow and alter light scattering. "