This environmental data-set consists of 56 sediment, 23 Cladophora and 23 water samples collected from beaches at Glen Haven, Good Harbor, Platte Bay and Esch road, located within The Sleeping Bear Dunes National Lakeshore, Leelanau and Benzie counties, Michigan. The data-set includes matrix type, location, date, and the qPCR reported value for each sample collected. Sample Collection and Processing: Samples were collected from Glen Haven, Good Harbor, Platte road and Esch road beaches in Sleeping Bear Dunes National Lakeshore. Sites were situated a short distance from stream or river inputs (except Glen Haven), and all sites had been associated with previous botulism outbreak events. Beach sediment, surface water, and Cladophora samples were collected from four sampling sites in SLBE from May to November 2012. At each site, surface water and beach sediment were collected from three locations, approximately 50 meters away from each other. Where available, sloughed Cladophora samples were collected from the beach or floating near the beach within the same range that sediment and water collected. Where applicable, samples were collected in triplicate as described in Wijesinghe and others, 2015. DNA Extraction: Sediment samples were collected in triplicate, composited into one sample and homogenized. Cladophora samples were collected as a single sample, in duplicate or in triplicate, composited into one sample and homogenized. Ten grams of sediment or Cladophora (wet weight) was used in each extraction per manufacture’s protocol (PowerMax® Soil DNA Isolation Kit. Mobio Laboratories, Carlsbad, CA). Water samples were composited, and one hundred milliliters of surface water was filtered through a polycarbonate filter. DNA was extracted per manufacture’s protocol, using a PowerSoil® DNA Isolation Kit used for water filters.