The article states the methodological foundation of effective deep-water mining in the Crimea. The authors observe the existing and possible interaction of technogenic systems during sea mining operations on the shelf sea and in the ocean with the fauna and flora. Accumulating data and establishing regularities may expect the formation of such a scientific discipline as sea mining. Sea mining is formed during investigating the object and its place in natural systems. The main scientific objectives of the off-shore mining technology include working out all the basic principles and methods of mineral resources mining from the sea.