Human diseases transmitted by freshwater organisms result in death or debilitation to millions of people annually. Malaria, lymphatic filariasis or elephantiasis, Japanese encephalitis, dengue (all transmitted through the bites of certain species of mosquitoes), onchocerciasis or river blindness (transmitted by certain black flies), and schistosomiasis or bilharzia (where certain snails serve as intermediate host) are the most important diseases associated with freshwater habitats. Mosquitoes are the most important human-disease vectors and can transmit nematode worms, viruses, and protozoans. Disease control strategies vary according to vector, disease-causing parasite, and type of water body. The latter include natural rivers and lakes, human-made water bodies such as reservoirs, and water holders in human settlements such as tires and containers. Vaccinations and chemotherapy are used to control the parasites; application of toxicants, the use of biological control agents, and habitat manipulations are used to control vectors. Large-scale control of freshwater, vector-borne diseases have ranged from the temporarily successful (malaria) to the highly successful (onchocerciasis and yellow fever). The biodiversity of the vectors, parasites, and the control agents, as well as the non-target organisms affected by control activities, have influenced both the spread and the control of human diseases associated with fresh waters.