Various changes were made throughout the Garden, including improvements for the Tropical Rainforest Conservatory and construction of the Aquatic Area where used to be a man-made Kenting beach before February, 2004. Other additions throughout the following years focused on increasing the variety of collections in the Garden. A Vine Garden, a Succulents Garden, a Lanyu Garden and a Taitung Cycad Garden were among the new gardens constructed. Other new features to the Garden included the Waterfall and the Orchid Bridge.
With increased attendance, the Botanical Garden of the Museum continued to grow in popularity and prestige.