This data release contains relative abundance data of the Clostridium botulinum neurotoxin type E gene (bontE) in sediment cores collected from three nearshore depositional basins near Sleeping Bear Dunes National Lakeshore (SLBE), Lake Michigan, in September 2010. Sediment cores were collected using a box corer and maximum collection depth ranged from 23 to 42 centimeters. Each sediment core was sectioned into 32 to 35 sub-core sediment samples and DNA for the detection of the bontE gene was extracted from each sub-core. Genomic DNA was analyzed for the relative abundance of the bontE gene in triplicates using quantitative polymerase chain reaction (qPCR) by the U.S. Geological Survey Michigan Bacteriological Research Laboratory in Lansing, Michigan. To validate the DNA extraction process and ensure quality control, laboratory blanks consisting of sterile nuclease-free water were extracted alongside sub-core samples during DNA extraction and results are provided in this data release. These data contribute to ongoing research on the historical occurrence and environmental drivers of bontE, a genetic marker for Clostridium botulinum type E toxin, in the Great Lakes.