Diesel, if allowed to stand will separate out the water, and the water will be in the bottom, eventually. Bacteria grow on the interface between the diesel and the water. So the main thing is to make sure that you have not already got water in the bottom of the tank/container. If you do, allow the fuel to stand undisturbed at least overnight, and remove as much as possible down to just above the water. Then remove the rest, plus as much water as possible down into a separate container (and preferably don't use this in an engine).
Then clean out and dry the container. How you do this is going to depend on the container - jerricans are easy - tip out as much out as you can, blow through with air for a while, then leave open in the sun for a hot dry day. Vehicle tanks vary from easy if there is a drain to difficult, and overhead storage tanks or underground tanks can be a real problem.
Next problem is to keep water out. Apart from getting water from storage, it mostly gets in by condensation from the air. This can be minimised by only having a small volume of air in contact with the fuel (keep your tank full!), moving inland, or sealing from the air, such as in a jerrican.
Consider what happens with a partly full tank. It cools overnight, and if the humidity reaches 100%, water condenses onto the exposed sides of the tank, runs down and ends up under the fuel. Next day, the air expands, pushing a lot of the dryer air out, only to be replaced as the next evening cools by a fresh lot of moist air, and the cycle repeats.
If the tank has very little air space, the amount of moisture that gets in is much leass, but also, the air tends to be kept warmer because it is in contact with the thermal mass of the fuel, which retains heat a lot better than the top of the tank.
Hope this helps,
John





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