AbstractThis study evaluates variations in petrophysical properties within a mixed alluvial to lacustrine carbonate system (Miocene, Madrid Basin, Central Spain). The transition from alluvial environments to lake margins settings displays a shift from alluvial, siliciclastic red sandstones and mudstones to palustrine–lacustrine mudstones to packstones. Fluctuations in lake‐water level enabled land plants to occupy the lake margins during periods of low lake levels. The palustrine carbonates include features like pseudo‐microkarst, nodular and mottled limestones; the lacustrine deposits include enlarged root cavities, desiccation cracks and channel bodies. Scarce fresh water biota comprises charophytes, gastropods and ostracods. The sediments possess high natural, irregular varying, gamma‐ray values at the alluvial–lacustrine transition, and low, but constant values at full lacustrine sites. Acoustic properties agree with lithological variations within individual facies. Porosity is the most important parameter influencing P‐wave and S‐wave velocities. The scatter in the velocity–porosity relationship links to the porosity type; macro‐porosity or microporosity. The wide range of pore types and pore sizes results in a weak porosity to permeability relationship for the carbonate‐dominated rocks with low permeability for microporous and high permeability for macro‐porous carbonates. The sandstones (probably only inhibiting interparticle porosity), and to a lesser extent the sandy wackestones to packstones, show quite a strong relationship between porosity and permeability. Elastic properties of mixed alluvial–lacustrine deposits (this study) and marine deposits (literature data) overlap as variations in pore structures and porosity values are similar. Only 16% of the marine and lacustrine carbonate sediments display Equivalent Pore Aspect Ratio values above 0.2. In travertine deposits, 83% of the samples exceed Equivalent Pore Aspect Ratio values above 0.2, which highlights that travertine deposits are dominated by larger Equivalent Pore Aspect Ratios compared to lacustrine and marine carbonate deposits. Travertines display other rock frameworks with different pore types, pore distribution and amount of porosity.