This paper assesses the options for control of malaria vectors through different water management practices in a natural stream in Sri Lanka. The association between water level in the stream and breeding of the immature stages of the primary vector Anopheles culicifacies was investigated and the feasibility of using existing irrigation infrastructure to reduce the breeding potential discussed. The most feasible option would be to implement a management routine where water is released periodically from an upstream reservoir to reduce the number of breeding sites downstream. This study indicates that by regulating the water level above 20 cm in the stream throughout the dry season the breeding of A. culicifacies could be significantly reduced. The intervention would have only limited impact on the water lost for agriculture and the management input would be minimal. However, for the intervention to work a high degree of support from the local community is essential and consultation between government departments needed.