This collection contains genetic extracts from surface water microbes collected during aquatic microbial sampling (NEON sample class: mic_dnaExtraction_in.amcDnaSampleID,mic_dnaExtraction_in.amcDnaOnlySampleID). Surface water metagenomic samples are collected at the same time and location as surface water chemistry samples once per month in wadeable streams (12 times per year) and every-other month in lakes and rivers (6 times per year). In wadeable streams, samples are collected near the downstream S2 sensor location. In lakes, samples are collected near the the 'buoy', 'littoral 1', and 'littoral 2' sensors, and sampling depth(s) is dependent on lake stratification. In rivers, samples are collected near the buoy sensor. The filters are frozen on dry ice in the field, and later are shipped on dry ice to an analytical facility for DNA extraction, sample preparation, and shotgun metagenomic sequencing (only for samples collected during July or August), marker gene sequencing (and subsequent analysis of community composition), and microbial abundance (qPCR). Laboratory metadata are then delivered to NEON for QC testing and acceptance, and then are formatted for upload to public sequence repositories. Details on sampling locations and timing are provided in the NEON document Surface Water Chemistry Sampling in Aquatic Habitats (https://data.neonscience.org/documents). Genetic extracts in 96-well plates from Battelle Applied Genomics are archived in the NEON Biorepository at -80 degrees Celsius. See related links below for protocols and NEON related data products. The DNA extraction and sequencing protocols used by Battelle Applied Genomics are available in the NEON document library (https://data.neonscience.org/documents).