There are two ways to sample a large amount of water on board.
1) Using water sampler (e.g. Niskin bottles): Water in specific depth(s) can be sampled. Also, environmental data can be obtained in combination with CTD.
2) From pump of ship: Surface water can be obtained from a tap the ship's continuous flow-through seawater system that is connected to a pump drawing water through the system in real time. (Caution! Not every ship or vessel has this pump system.)
Sampled water should either be filtered immediately or treated with benzalkonium, kept cool until back to laboratory.