You will want to periodically check that your hatches are watertight. We use a very durable sealant for our bulkheads, but the flexing that occurs during transport and paddling may wear them out over time.
If your storage compartments are wet, first identify where the water is getting in. Are your hatch covers intact and securely fastened? Are your bulkheads sealed well? Are there any deck fittings that have broken or become loose? If the source isn’t obvious, do a "reverse leak test." Begin with a dry boat. Put about a gallon of water in the suspect hatch, seal the cover, then roll the boat around and see where the water comes out. If the leak is coming from a bulkhead, simply clean and dry it, then simply reseal it with a good marine sealant such as Lexel, 3M 5200 or Sikaflex. DO NOT use silicone as it does not stick well to plastic or composite materials. Replacement deck fittings and neoprene washers are available for deck leaks.
Remember to use dry bags for items that MUST stay dry.