Abstract1. Tropical aquatic ecosystems are species rich, with high numbers of endemics. Increasing pressure from human activities, including demands for food and energy, growing human population, and economic aspirations, highlights the need for a more concerted effort towards aquatic conservation.2. Understanding of tropical aquatic ecosystems has developed largely from a northern temperate perspective that might not be always appropriate. Applying classic models of how water bodies function can hinder effective conservation strategies. This is coupled with very incomplete knowledge of species distributions and their ecology.3. Better understanding of tropical aquatic ecology to guide conservation needs a research agenda that connects more strongly with the social‐ecological realities of tropical ecosystems.4. Although approaches to conservation may be contested, a fundamental challenge to protection of aquatic habitats is a lack of capacity at the individual and institutional level. Without this, the development of improved techniques and approaches for tropical aquatic conservation will fail to reverse current trends of degradation. Research outputs on tropical aquatic ecosystems remain dominated by institutions based outside the tropics.5. Building awareness and practice to conserve the aquatic ecosystems of the tropics can be supported through extending the dialogue across sectors and by connecting tiers of governance. An ecosystem services framework that identifies the benefits that humans derive from ecosystems provides a powerful tool, often linked with estimates of economic value. However, this can neglect important regulating services or distract from more fundamental existence value.6. The preservation of tropical aquatic diversity will only be achieved if recognized as important at all levels, from local to global. Targeted external support can build awareness and capacity, but conserving aquatic ecosystems requires local commitment. Developing community monitoring that provides straightforward information on ecosystem health presents opportunities to connect citizens with the ecosystems that, ultimately, they depend on. Copyright © 2016 John Wiley & Sons, Ltd.
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