Abstract. Karst water resources play an important role in drinking water supply but arehighly vulnerable to even slight changes in climate. Thus, solid andspatially dense geological information is needed to model the response ofkarst hydrological systems to such changes. Additionally, environmentalinformation archived in lake sediments can be used to understand past climateeffects on karst water systems. In the present study, we carry out amulti-methodological geophysical survey to investigate the geologicalsituation and sedimentary infill of two karst lakes (Metzabok and Tzibaná)of the Lacandon Forest in Chiapas, southern Mexico. Both lakes present largeseasonal lake-level fluctuations and experienced an unusually sudden andstrong lake-level decline in the first half of 2019, leaving Lake Metzabok(maximum depth ∼25 m) completely dry and Lake Tzibaná (depth∼70 m) with a water level decreased byapprox. 15 m. Before this event, during a lake-level high stand inMarch 2018, we collected water-borne seismic data with a sub-bottom profiler(SBP) and transient electromagnetic (TEM) data with a newly developed floatingsingle-loop configuration. In October 2019, after the sudden drainage event,we took advantage of this unique situation and carried out complementarymeasurements directly on the exposed lake floor of Lakes Metzabok andTzibaná. During this second campaign, we collected time-domain inducedpolarization (TDIP) and seismic refraction tomography (SRT) data. Byintegrating the multi-methodological data set, we (1) identify 5–6 mthick, likely undisturbed sediment sequences on the bottom of both lakes,which are suitable for future paleoenvironmental drilling campaigns, (2)develop a comprehensive geological model implying a strong interconnectivitybetween surface water and karst aquifer, and (3) evaluate the potential of theapplied geophysical approach for the reconnaissance of the geologicalsituation of karst lakes. This methodological evaluation reveals that underthe given circumstances, (i) SBP and TDIP phase images consistently resolvethe thickness of the fine-grained lacustrine sediments covering the lakefloor, (ii) TEM and TDIP resistivity images consistently detect the upperlimit of the limestone bedrock and the geometry of fluvial deposits of a riverdelta, and (iii) TDIP and SRT images suggest the existence of a layer thatseparates the lacustrine sediments from the limestone bedrock and consists ofcollapse debris mixed with lacustrine sediments. Our results show that thecombination of seismic methods, which are most widely used for lake-bottomreconnaissance, with resistivity-based methods such as TEM and TDIP cansignificantly improve the interpretation by resolving geological units orbedrock heterogeneities, which are not visible from seismic data. Only the useof complementary methods provides sufficient information to developcomprehensive geological models of such complex karst environments