A chorine tablet dropped in it.
I would give it a really good flush and clean and vacum out with a wet/dry vac and clean it again with a good detergent. I assume the water is just apart of the boat design you have?? If it is from a prop gland, you can lesson the area of containment by biulding a small dam box under the gland to capture the water and a small bilge pump
and float switch in side it. A shower sump
box does well at this task. That way the main water ingress is contained the the larger bilge
area can be kept dry and clean. Keep the main bilge pump
where it is for emergencies.