This paper reviews the nature of substrate vibration within aquatic environments where seismic interface waves may travel along the surface of the substrate, generating high levels of particle motion. There are, however, few data on the ambient levels of particle motion close to the seabed and within the substrates of lakes and rivers. Nor is there information on the levels and the characteristics of the particle motion generated by anthropogenic sources in and on the substrate, which may have major effects upon fishes and invertebrates, all of which primarily detect particle motion. We therefore consider how to monitor substrate vibration and describe the information gained from modeling it. Unlike most acoustic modeling, we treat the substrate as a solid. Furthermore, we use a model where the substrate stiffness increases with depth but makes use of a wave that propagates with little or no dispersion. This shows the presence of higher levels of particle motion than those predicted from the acoustic pressures, and we consider the possible effects of substrate vibration upon fishes and invertebrates. We suggest that research is needed to examine the actual nature of substrate vibration and its effects upon aquatic animals.