Abstract: The object of the research is the geophysical processes in the ocean, in particular, distribution and transformation of internal waves in stratified fluid. According to the author, it is possible to study such large-scale processes using the methods of numerical modeling and open hydrological data sources. Nevertheless, numerical experiments require accompanying software tools. These tools include means of incoming data processing, software presentation methods in a form of networks, data sample preparation methods, data visualization means, and methods of initialization of mathematical models. The author examines all stages of a numerical experiment and required software tools as well as aspects of initialization of numerical models. The author demonstrates that part of the initial conditions can be created from the data context in an automatic mode. The novelty of the research is caused by the fact that the author offers methods to be used to create problem-oriented software tools to carry out a numerical experiment on modelling geophysical processes that depend on spatiotemporal distribution of multivariable data. The methods offered can be used in many spheres of mathematical modelling of physical processes such dependencies are attributable to.