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In recent years the world has been actively developing oil and gas fields on the shelf, including in seismically active areas. On the seabed it is very difficult to carry out qualitative geological and geophysical studies and seismological observations in full, which are a part of seismic microzoning works. Programs for computational methods during seismic microzoning allow taking into account nonlinear soil properties. In the article the experience of studies on seismic microzoning (2012–2015) for the installation area of offshore structures on the shelf of the Middle Caspian Sea is considered. In conditions of absence of observations by bottom seismic stations the possibility of seismic hazard assessment by computational methods taking into account local soil conditions is shown. Thus the obtained values of seismic intensity are lower in comparison with the results of estimations by method of engineering and geological analogies and method of seismic rigidity. Maximal impacts from zones of possible earthquake sources most dangerous for Middle Caspian Sea have been taken into account by peculiarities of spectral composition of vibrations of ground bases in the form of reaction spectra.