Abstract: The investigation of the Baiyangdian lake bottom strata holds significant practical importance for the ecological geological survey, ecological silt removal, and wetland ecological protection of Baiyangdian. In order to systematically identify the stratigraphic structure of Baiyangdian lake at a regional scale and provide accurate target data support for drilling investigations, this paper introduces an innovative application range of ground penetrating radar (GPR) and conducts a ship-based stratigraphic survey through the water body. This study analyzes the technical challenges associated with exploring the lake bottom structure using GPR. It examines the characteristics of electromagnetic wave propagation and geophysical response conditions in two scenarios: with sediment and without sediment. A simplified model is established, consisting of diaster-water + silt layer + lake bottom primary formation. By comparing the exploration capability and adaptation conditions of different hardware equipment of mainstream ground penetrating radar systems at home and abroad, this paper optimizes the working mode by employing double kayaks equipped with a 50 MHz low-frequency combined antenna. Additionally, it combines suitable data processing technology for extracting weak signals from underwater electromagnetic waves. As a result, stratigraphic structure data at a depth of 15m are obtained for Baiyangdian lake. The findings indicate that this model is applicable to areas within the lake where water depth is less than 5 m; here, weak reflection characteristics are observed in electromagnetic waves emitted by primary formations at the lake bottom along with 2 ~ 3 groups of sand reflection interfaces at depths up to 15 m. The presence of silt layers significantly attenuates electromagnetic wave reflection intensity originating from primary strata at the lake bottom.