An acoustic sounding method for studying the distribution of bubbles and the structure and dynamics of plankton communities in the surface layer of the South China Sea is shown. The possibility of using the sounding method based on nonstationary and nonlinear sound scattering is discussed. Estimates are made of the biomass distribution in zooplankton assemblages along long tracks in the South China Sea. The results obtained indicate a high concentration of plankton in the surface layer of the sea, which is comparable with the most productive areas of the World Ocean. It is shown that in the northern part of the South China Sea and off the coast of Vietnam, the concentration of plankton increases dramatically. The presence of large bubbles and a smooth decline of the size distribution function were found to be characteristic only of the waters of the South China Sea, in contrast to similar characteristics of tropical waters of the Pacific Ocean.