The easiest and cheapest way to get from Kratie to Koh Trong island, other than to swim, is to catch the ferry. From the main river front road in Kratie look for the Jasmine Boat Restaurant which is located right next to the boat dock, then take the steep steps down to the jetty. The boat starts running around 6 am and the last boat is any time between 5 pm and 5.30 pm.
A one way trip costs 1000 Riel per person, a bicycle is an additional 500 Riel, and should you wish to haul down a motorbike it will cost 1000 Riel. Although it is possible to take a bike we wouldn't recommend it as certainly much better and easier to hire one from the information centre once you've arrived on Koh Trong island.
The journey takes about 10 minutes and the boat will run once it is full. This means at certain times of day the regularity can be a little unpredictable. Notably the journeys are frequent in the morning and late afternoon and less frequent during the very hot hours in middle of the day.
You can purchase cold drinks on the boat too, just look for the large orange cooler box - water is 500 Riel and soft drinks 2000 Riel.
The family who operate the ferry have several different boats; most frequently the small boat is used and a larger front loading boat is operated during very busy times such as Khmer New Year in April. That being said at present the large boat is in operation.
If you're unfortunate enough to miss the last boat in the afternoon you can always hire it for a private trip back to town for $10, or even better book into a homestay and enjoy the sunset and a quiet night on the island.