1. Species diversity is declining more rapidly in freshwater ecosystems than in any other, but the consequences for genetic diversity, and hence evolutionary potential, are poorly understood. In part this reflects limited use and development of modern molecular tools and genetic approaches to address conservation questions in rivers, lakes and wetlands. As widespread, diverse and functionally important organisms, freshwater macroinvertebrates are ideal candidates for genetic approaches to reveal, for example, the conservation consequences of demographic histories and past disturbances. However, the availability of microsatellite markers for this group is very limited. 2. Using next generation sequencing, microsatellite markers were developed for Isoperla grammatica (Poda, 1761), Amphinemura sulcicollis (Stephens, 1836) and Baetis rhodani (Pictet, 1843) to enable conservation genetic investigations of these widespread invertebrate species. Fifty-two robust microsatellite loci were developed (18, 21 and 13 per species), all with high levels of allelic diversity (7-27, 3-16, 5-13 alleles per loci, respectively). 3. These tools will allow assessment of genetic structure, dispersal and demographic resilience in these model species as a function of environmental change and variation, thereby aiding freshwater monitoring and conservation. The authors urge further capacity building to support genetic applications to the conservation biology of other aquatic organisms. Copyright # 2016 John Wiley & Sons, Ltd.