To assess the variability of low-abundance oligonucleotide detection across sample matrices, we spiked DNA reference standards (meta sequins) into replicate wastewater DNA extracts at logarithmically decreasing mass-to-mass percentages (m/m%) and deeply sequenced them on the Illumina platform. This dataset summarizes the experimental conditions and results of the detection frequencies of those oligonucleotides as well as detailed descriptions of the DNA reference standards used. This dataset is associated with the following publication: Davis, B., P. Vikesland, and A. Pruden. Evaluating Quantitative Metagenomics for Environmental Monitoring of Antibiotic Resistance and Establishing Detection Limits. ENVIRONMENTAL SCIENCE & TECHNOLOGY. American Chemical Society, Washington, DC, USA, 59(12): 6192-6202, (2025).