There are marine crossings from Colombia to Panama and Ecuador.
Numerous sailboats operate between the Panamanian ports of Portobelo, Porvenir or Colón and Cartagena. This is a popular form of intercontinental travel, and generally passes through (and stops in) the beautiful San Blas Islands along the way. Some boats operating from Cartagena's yacht clubs work on a fixed schedule, others leave when full. The entire Cartagena–San Blas–El Porvenir trip by sailboat costs between US$450 and US$650 all-inclusive, with the majority of boats charging US$550. From El Porvenir, you'll need to carry on by speedboat to Carti or Miramar, from where you can continue overland to Panama City; or you can fly from El Porvenir.
Boats have traditionally been unregulated and safety is an issue. Cartagena-based Blue Sailing, a Colombian-American agency, has begun to change that in recent years. At the time of research the company represented 25 boats, and it ensures they all have proper safety equipment for open sea navigation, monitor the boats’ locations 24 hours a day and uses only licensed captains.
Another possible departure point for Panama is the small Colombian town of Capurganá, from where it's possible to catch a 30-minute boat ride to Puerto Obaldía, followed by a short flight to Panama City.
It is also possible to arrange transportation from Bahía Solano to Jaqué in Panama, although boats are very infrequent. From Jaqué you can continue along Panama's Pacific coast to Panama City, or fly.
It is possible to cross the border via skiff along the Pacific coast near Tumaco, but security along the road to Tumaco and the security situation in the city itself make it a place for travelers to avoid.