The Sikorsky S-42A “Dominican Clipper” originated in Miami, FL and was bound for Rio de Janeiro, Brazil with en route stops at Antilla, Port-au-Prince, San Pedro de Macor¡s, San Juan, Port of Spain, Paramaribo, Belem, Camacin, Recife, Salvadore and Victoria. During the leg from Macoris to San Juan the airplane encountered head winds which resulted in a trip that took 1 hour and 40 minutes longer than planned. Naval surface boats and aircraft were anchored at San Juan harbor, preventing the use of the regular landing area. During the night landing outside the harbor the airplane porpoised and it struck a swell, causing the plane to rise. Just as power was applied, the left pontoon struck the water. The nose then struck the water and the S-42 waterlooped, coming to rest in a partially submerged position. PROBABLE CAUSE: “Porpoising of the aircraft off the water in a stalled attitude from which recovery was not accomplished.” Contributing factors: 1. Congested condition of the San Juan harbor which necessitated a landing outside of the protected area. 2. Unforeseen change in wind direction subsequent to departure of the trip from Macoris and the change in sea conditions as the trip neared San Juan, at which time there was insufficient fuel on board the aircraft to return to Macoris. 3. An attempted landing during darkness under adverse weather and sea conditions and with limited facilities for night operation. 4. Failure if Pan American World Airways, Inc seaplane tender crew to transmit information to the pilot of the aircraft concerning the steadily increasing amplitude and intensity of the swells in the landing area. 5. Lag in communication between the flight crew and the San Juan ground station due to the inherent slowness of radio telegraph transmissions and reception.