Abstract. The present geophysical study was motivated by the need to determine suitable coring locations for paleolimnological studies in two karst lakes (Metzabok and Tzibaná) of the Lacandon Forest in Chiapas, southern Mexico. We used seismic and transient electromagnetic methods to map the sediment thickness below the lake floor. When lakes were filled in March 2018, we collected seismic data with a sub-bottom profiler (SBP) and transient electromagnetic (TEM) data with a floating single-loop configuration. The latter aimed at assessing the TEM method as an alternative to seismic methods for the investigation of lake sediments and geology. After the first campaign, water levels of both studied lakes dropped dramatically by July 2019, leaving Lake Metzabok (maximum depth ~ 25 m) dry and Lake Tzibaná (~ 70 m) with a water level decreased by approx. 30 m. After the sudden drainage of the lakes, we complemented water-borne measurements by a survey carried out on the exposed lake floor in October 2019, when lake levels were still low. During this second campaign, we collected time-domain induced polarization (TDIP), and seismic refraction tomography (SRT) data on the desiccated bed of Lake Metzabok and some dry parts of Lake Tzibaná. By comparing the various data sets, we find that (i) SBP and TDIP phase images consistently resolve the thickness of the fine-grained lacustrine sediments covering the lake floor, (ii) TEM and TDIP resistivity images consistently detect the upper limit of the limestone bedrock and the geometry of fluvial deposits of a river delta, and (iii) TDIP and SRT images suggest the existence of a layer that separates the lacustrine sediments from the limestone bedrock and consists of collapse debris mixed with lacustrine sediments. While our results do not imply that resistivity-based methods could generally replace seismic reflection surveys for lake-bottom reconnaissance, they clearly show that TEM and TDIP surveys can provide important complementary information and resolve additional geological units or bedrock heterogeneities.