old diesel fuel
After three years there is a good chance that there is more than fuel living in your tank now. This is especially true if the tank was not completely full when you put the boat in storage. The constant expansion and contraction of the air in the tank (due to temperature changes) brings a fresh batch of moisture laden air into the tank like clockwork. Much of that moisture ends up as water in your tank.
In addition to getting the fuel out of the tank you should probably try to clean the tank up a little, too.
How to do this depends on the design of the tank. If you are lucky enough to have an inspection plate I suggest working though it. I had to use the fuel gauge hole on my NorSea 27.
I used a drill powered pump attached to a piece of pvc pipe that was long enough to reach the corners of the tank. I pumped the fuel into a plastic soda bottle (big one, obviously) so that I could see what was coming out. I would then empty the soda bottle into a jerry can. I removed about 10 gallons this way and then let the fuel in the jerry can sit for a few hours and decanted the clean part back into the tank and did the whole process again.
Actually what I did was reverse my pump and shoot the decanted fuel back in to try and stir up any crud in the bottom.
After the second flushing I did not see any more "stuff" coming out in the fuel and pronounced it clean.
A local marina had a tank for the proper disposal of the dirty fuel.
I would probably also flush the lines up to the injection pump and change the filter on the engine in addition to the secondary filter.
there are also commercial fuel scrubbing services that can do a much more through job but when I checked out the pricing they only seem like they would be economical if you had a few thousand dollars in fuel in the tanks and you were not willing to throw the dirty fuel away.