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Tagged neutron inspection system was used for the underwater detection of explosives. Neutrons were produced in the d+t nuclear reaction with API 120 sealed tube neutron generator. Five kilograms of TNT explosive were measured in a pool filled with water. Measurements were done in target in, target out configuration. Also, a sandwich made of 6 mm thick iron plates with explosive placed between two layers of sea sediments was measured under the same conditions. Sediments were collected in the Adriatic Sea. Measurements were repeated with TNT explosive replaced by rocks of similar size and shape. Neutron tube was rotated in order to find the position of explosive (rocks) in the sandwich. It was found that TNT can be detected underwater and that is possible to distinguish TNT from the sea rocks placed between 6 mm thick iron plates or between layers of sediments by their ratios of carbon and oxygen.