The sampling effect may reflect artifactual trends in species richness and distribution across various spatiotemporal scales. The paper aims to examine how sampling frequency impacts the observed community dynamics in groundwater habitats of the unsaturated zone of the Ciur Izbuc cave (northwestern Romania) and addresses data interpretation biases that can arise when different sampling strategies are applied. The patterns obtained by monthly sampling over a year were compared with the patterns from the seasonal samplings over 4 years and with those from sampling conducted at an interval of 2 days over 1 week. Sample-based rarefaction curves were computed to compare estimated species richness between datasets with different sampling frequencies. Self-organizing maps were used to explore the impact of sampling frequency on depicted patterns over various temporal frames. Sampling frequency contributed to contrasting species richness, abundances and spatiotemporal dynamics of copepods in the studied groundwater habitats across scales. Monthly sampling and seasonal sampling revealed maximum number of species (seven) and led to stable species estimates after 11 sampling occasions and 12 sampling occasions, respectively, while 1 week of every-other-day sampling was not enough to capture the highest number of species. Spatial heterogeneity of species distribution increased over 4 years of seasonal sampling. Our results demonstrated the importance of sampling rate and temporal frames in understanding depicted aquatic community dynamics a must before drawing conclusions. We advocate cautious data interpretation and pattern generalization in groundwater ecology to avoid hasty assessments of community changes across spatial and temporal scales.