Karst aquifers are complex systems characterized by high heterogeneity and anisotropy. Karst hydrological duality is evident in processes such as recharge, storage, and flow. The MODFLOW Conduit Flow Process (CFP) simulates this flow duality. In this study, CFP version 2 (CFPv2) was applied to the Yucatan karst in Mexico, known for its well-developed karst features, including subsurface conduits. Given the sparse data regarding the three-dimensional location and connectivity of conduits and underwater coastal springs, the theoretical conduit pathways were inferred from geology or geophysics. CFPv2 was utilized to evaluate these theoretical conduit network arrangements based on indirect data from gravimetry, geophysics, and geological information from the second-largest impact crater on Earth. The Merida Metropolitan Area (a densely populated region in the Mexican state of Yucatan) was selected as the study area. Piezometric data from 43 monitoring wells (collected during the monitoring period 1996–2001) formed the basis for model inversion. Recharge volumes were derived from precipitation data collected from 14 climatic stations. Results were compared with a previous groundwater flow model applied in the same area utilizing the CFP Mode 2, a turbulent flow-enabled single continuum model. Results of this study support the hypothesis of multirings of preferential flow influencing groundwater dynamics, providing important insights regarding the sub-surface in this karst region.