This study analyzed and presented zooplankton species occurrence, diversity distribution, and community composition in ninety lakes across South Korea using samples collected through the “Survey of Lake Aquatic Ecosystem Status and Health Assessment.” When comparing our results with the National Species Checklist, we identified factors within each of the three taxa that warrant improvement due to their influence on diversity assessments. To bridge the gap between the ongoing lake ecosystem surveys and the continually updated National Species Checklist-and to enhance the accuracy of diversity evaluations-we conclude that (1) greater taxonomic rigor must be reflected in the national checklist, and (2) the limitations of morphology-based identification (α-taxonomy) must be addressed. Because the National Species Checklist does not distinguish among species, subspecies, and morphospecies, it can give rise to taxonomic oversplitting and taxonomic inflation, leading to ambiguous diversity-index results. Moreover, the low resolution of morphological identification for zooplankton (at the genus, family, or class level) can introduce errors when comparing communities across habitats or detecting non-native introductions. Although alternatives such as environmental DNA and functional diversity exist, they require further refinement before being adopted in policy; therefore, they should be implemented alongside and in comparison with current aquatic ecosystem health assessment methods.