The Aviary is a cage pen where InGen housed pterosaur species. Because the InGen scientists assumed that pterosaurs lived near flowing water (as their diet consisted of fish), the cage was built over the Isla Nublar river.
The Aviary scene did not ultimately appear in the first Jurassic Park film. However, during the Lunch Scene in the VIP dining room concept art of the Aviary was ultimately displayed on one of the slideshow boards. It briefly shows the outer structure of the visitor booth.
In The Lost World: Jurassic Park, a wall painting can be seen in the Worker Village. It clearly is a painting of the Park on Isla Nublar. In the left corner a pterosaur can be seen, proving that an aviary was built or planned to be built in the Park.
Construction of Jurassic Park
During the planning, it was decided to put the Pteratops Lodge inside the paddock because the designers thought the inhabitants would be "safe" for tourists to interact with. However, this did not go well back then, it turns out the Cearadactylus were ill-tempered and attacked many maintenance crews that worked on it, thus leaving the lodge derelict inside.
Isla Nublar Incident
During the power outage, the dinosaurs escaped but the Cearadactylus were stuck inside. When Alan Grant, Lex Murphy and Tim Murphy were escaping the Cearadactylus during the outage, they took a raft and headed downstream towards the paddock. However, they had no idea what was going to happen. Consequently, the Cearadactylus attacked them, but luckily they were able to escape from them.
It can be assumed that the lodge and the aviary were both destroyed when the Costa Rican Air Force bombed the island.