A system for processing samples from a body of fluid. The system includes one or more sample bottles for acquiring a sample from the body of fluid. Each sample bottle initially retains a pre-filling fluid. Each sample bottle includes a fluidic inlet port and a bottle outlet port. Each sample bottle has an inlet check valve coupled to the fluidic inlet port, the inlet check valve configured to allow fluid from the body of fluid into a sample bottle via the fluidic inlet port when the pressure difference between the body of fluid and fluid within the sample bottle reaches a threshold. The system further includes at least one pump, the bottle outlet port of each sample bottle selectively coupled to the at least one pump via a different control valve. The at least one pump is configured, in a first configuration, to remove prefilling fluid from each selected sample bottle such that, for each selected sample bottle, the pressure difference threshold is reached and a sample from the body of fluid is acquired.