The name of the film you remember is "Captain Korda". You didn't recognize it from the CCFF page because the original summary I provided (from the TV Guide) was really off! The film is Czech, and as you remembered, much of it took place near water.

The boy's name was Joey. He was sent from a children's home to live with Mr. and Mrs. Korda. He was happy there, but his birth mother decided she wanted him back.

The Kordas returned the boy to his mother, but Joey was very unhappy there with his new stepfather. The final straw is when his stepfather tears apart a boat that Mr. Korda built for Joey and uses it to patch the barn.

Joey runs away and falls asleep near the railroad tracks. His mother eventually calls Mr. Korda and admits that Joey would be better off with him. Mr. Korda finds the boy and takes him home for good, promising to build him another boat.

Unfortunately, I haven't been able to get any leads on whether this film is available commercially on VHS or DVD. Apparently this was a popular broadcast in Germany, under the name "Haifischorden für den Kapitän "; there are people there looking for it, also.

Thanks, Phil. I updated the entry on the main CCFF page.