Such deposits begin as living colonies with natural 'adhesives' to help them 'stick' to the surfaces. Its when the cells die and break off from colony or when large portions of the colony breaks away is when the 'trouble' begins. You really have to visualize to be sure of the complete removal; otherwise, its just a 'guess'.
You can use chemical tank cleaners such as: Star brite - Catalog - Product Detail
.... but unless you direct visualize, you can never be 'sure'.
To lessen and minimize contamination: keep the MINIMUM amount of fuel in your tank; dont always 'top-off' as there is NO BENEFIT in storage of 'old' fuel; diesel and gasoline have relatively short 'shelf life' when in contact to atmospheric air); use 'fresh' fuel (from a high-turnover 'truckstop', etc.); drain/empty the tank when the boat is not being used for looooong periods such as winter storage.
BTW - Atmospheric water 'equilibrates' or 'saturates' into fuels (typically through the tank vent); the less amount of fuel - the less water 'uptake'. ;-)