Any many other microorganisms including Leptospira.
The latter can be acquired through the skin by swimming in the wrong areas in Hawaii [1]. Giardia can be difficult to treat and give you horrible problems for years as happened to one friend. Another friend acquired boils with visible nematodes under the skin from wading near Belem in Brazil. As a field biologist one is constantly reminded that nature is not benign. However local knowledge can usually keep one out of trouble, with the disclaimer that sadly in almost all of the world even its wildest most remote corners, the organism that poses the greatest danger is Homo sapiens.
1 http://health.hawaii.gov/about/files/2013/06/leptobrochure.p...