Water in counter top seams is as bad as water on the floors; it wrecks the particle board used in their construction. Home improvement centers carry a variety of seam sealers.
The sooner you notice the problem and repair it the better off you will be. If it goes untreated the counter will have to be replaced because none of the patch, re-glue, etc. tricks will work where the particle board has failed.
You may notice a bad seam when the counter top starts to sag, or when the laminate begins to peel. At this point it may already be too late to save the counter. It is probably best to start shopping for replacements.