Working in a variety of media, from film and photography to sculpture and installation, Lothar Baumgarten creates works that speak to central themes of the environment and civil rights, inspired by the landscape and civilizations of the indigenous peoples of South America. Much of his work is influenced by his explorations of the Amazon, particularly the destruction of its rainforest and the erasure of the area's indigenous cultures by European settlers. Terra Incognita—whose title is drawn from the name given to the Amazon basin five centuries ago by explorers—is an installation that the artist has revisited in five versions, based upon his experience living among the Yanomami Indians in the Amazonian jungle between 1978 and 1980. Plates are balanced on or near islands of wood as electric wires and light bulbs in blue and yellow connect them in a maze, reminiscent of the vast network of rivers and tributaries of the Amazon basin. Drawings on the plates are like maps, as the blue and yellow lights refer to both the beauty of the forest and the diseases introduced by invaders. Baumgarten describes the dynamic in his work as a critical discourse where "contemporary culture unfolds within an architectural framework. The content becomes the form." He explains, "My critical approach does not intend to offer autobiographical solutions to universal problems. I believe art should encourage us to question the status quo and the structures that allow it to persist."

Baumgarten has had exhibitions at institutions including the National Museum of Modern Art inTokyo, the Royal Botanic Garden in Edinburgh, the Stedelijk Museum in Amsterdam, Los Angeles' Museum of Contemporary Art, and the Solomon R. Guggenheim Museum, among many others.