Abstract Freshwater shrimps are abundant in several rivers and streams of Puerto Rico. These species provide many ecosystem services, including cycling nutrients, connecting coastal and montane ecosystems, and serving as food for other organisms. Tracking the movements of individual shrimp is necessary to understand their responses to environmental and anthropogenic disturbances. To explore methods of measuring movement, we conducted two types of lab experiments. The first measured the acute and chronic responses of Xiphocaris elongata (Guérin-Méneville, 1855) and Atya lanipes (Holthuis, 1963) to visual implant tags. Daily observations showed 100% survival, and video analysis of movement metrics (percent active time, total distance moved, and mean velocity) revealed no significant differences between tagged and control shrimp. The second experiment assessed the response of A. lanipes to passive integrated transponder tags. These shrimp showed low survival, independent of size. This study supports the use of visual implant tags but recommends further study before utilizing passive integrated transponders to mark these small shrimp species.