Geophysical logs were collected and analyzed along with bedrock core samples and bedrock outcrops to define the bedrock stratigraphy and flow zones penetrated by 93 monitor and water-supply wells in Cayuga County, New York. The work was completed from 2001 through 2011 as part of an investigation of volatile-organic compound contamination in the carbonate-bedrock aquifer system between Auburn and Union Springs. The borehole logs included gamma, caliper, wellbore image, fluid property, and flow logs. The log information was used with bedrock core samples to define the regional stratigraphy, evaluate flow zones within the bedrock aquifers, and develop and implement a multilevel monitoring design for groundwater levels and water quality within the study area.