Wood density (relative to water) determines whether it will sink or not. Some wood is naturally more dense than other woods, iirc, by factors of 10-20+ times. In addition, live wood contains liquid in many of it's cells, while dead wood contains a lot more air in it's cells. As wood sits underwater for a long time, water fills the cells and makes the wood item more dense, and more likely to sink.
Drilling holes in the wood will not work but submerging the wood under water for long periods of time will work as water pressure will slowly force air out of the wood and replace it with water. However, extremely light wood (which starts at a naturally low density) just might never sink in water unless accompanied by weights.