Recognising both the importance of intertidal wetlands and their role in mosquito-borne disease we discuss wise management to conserve wetland values and to reduce vector borne disease health risks. First we summarise the mosquito-borne diseases associated with intertidal wetlands in sub-tropical and tropical Australia. We consider the Ramsar Strategic Plan, its reflection in some key Australian statutes and the relationship between environment-focussed legislation and health legislation. This is followed by a brief overview of mosquito control and its impact on human health. Using a salt marsh example of an integrated process, we describe the development of what was, in the 1980s in Australia, a novel method of habitat modification (runnelling) for mosquito control. Runnelling modifies the tidal water flow on salt marshes, reducing mosquito larval numbers and minimising environmental impacts. The approach is related to two of the Ramsar goals (wise use and institutional capacity and effectiveness). We then describe the extension of its rationale to a complex mangrove system. Finally, with a concept model, we consider the convergence between minimal habitat modification for wetland conservation and human health protection using an interdisicplinary approach involving multiple stakeholders.