Geophysical anomalies above the different deposits, such as sulfide orebodies, kimberlite pipes, as well as anticline structures with reservoirs of oil and gas, are well studied by geophysicists. At the same time, there are complicated problems in reveal the anomalies related to structures controlling the depositional areas. The applied procedures are aimed at revealing of peculiarities of magnetic and gravity fields near deposits. The method includes a double Fourier spectrum study of gridded anomaly magnetic and gravity fields, followed by filtration and transformation of potential fields. At the next stage the maps of transformed fields are analysed by means of moving windows. In the final stage of interpretation, parameters are defined whose relationships to deposits are valid. We illustrate our approach on the real data examples from the Yakutia diamond-bearing kimberlite fields, Norilsk copper-nickel deposits, and oil/gas fields in western Siberia.