Reliable fish tagging methods are needed to conduct studies (e.g., movement, habitat, abundance) that inform conservation and management decisions; however, dependable tagging approaches are lacking for many small-bodied fishes. Therefore, our study objective was to determine survival, tag retention (visible implant elastomer [VIE], PIT, or light-activated microtransponder [“p-Chip”]) and tagging effects on short-term growth of the federally threatened Arkansas River Shiner Notropis girardi. We also examined the use of anesthesia to reduce fish mortality (i.e., reduce handling time) and improve tagging efficiency. Fish tagged with p-Chips had the highest survival (87%), whereas VIE-tagged fish had the second highest survival (67%). Visible implant elastomer tags were retained in our fish 88% of the time, and retention was also high using p-Chips (72%). Location of the VIE tag did not significantly affect survival or retention rates. Survival of PIT-tagged fish significantly increased from 53% to 83% when handling time was reduced; however, tag retention was relatively low in both cases (50% and 45%, respectively). The majority of tagged fish across experiments (83–100%) gained weight regardless of tag type. If the research or management goal is to tag Arkansas River Shiner or similar species with individual identification, p-Chips appear to be an appropriate tag. Particularly if cost is limiting or higher tag retention is needed, VIE tags would also be appropriate for batch tagging (i.e., no individual identification). Additional studies to broaden application of tagging to other small-bodied species would be beneficial