Motivated by recent global initiatives for biodiversity conservation and restoration, this article reviews the gaps in our understanding of, and the challenges facing, freshwater macroinvertebrate biodiversity and conservation in tropical regions. This study revealed a lack of adequate taxonomic, phylogenetic, and ecological information for most macroinvertebrate groups, and consequently there are large-scale knowledge gaps regarding the response of macroinvertebrate diversity to potential climate change and other human impacts in tropical regions. We propose ideas to reduce the impact of key drivers of declines in macroinvertebrate biodiversity, including habitat degradation and loss, hydrological alteration, overexploitation, invasive species, pollution, and the multiple impacts of climate change. The review also provides recommendations to enhance conservation planning in these systems (as well as providing clear management plans at local, regional, and national levels), integrated catchment management, the formulation of regulatory measures, the understanding of the determinants of macroinvertebrate diversity across multiple scales and taxonomic groups, and the collaboration between researchers and conservation professionals. It is suggested that the integrated use of macroinvertebrate biodiversity information in biomonitoring can improve ecosystem management. This goal can be facilitated in part by conservation psychology, marketing, and the use of the media and the Internet.