The carbonate-mudstone-dominated Lower Cretaceous Agrio Formation is the youngest marine source rock of the hydrocarbon-prolific Neuquén Basin in Argentina, yet its facies variability and unconventional hydrocarbon potential remains relatively understudied. Detailed studies of mudstone facies variability in thick, carbonate mudstone successions deposited largely below storm wave base (i.e., chalk–marl, black shale, limestone), like the Agrio Formation, are rare and instead commonly focus on biostratigraphy or organic geochemistry alone. A continuous northern section of the Agrio Formation and a southern composite section of the lower Pilmatué and middle Avilé members, totaling ∼ 1,200 m of outcrop, were measured. From these measured sections, programmed pyrolysis (n = 339 samples), X-ray diffraction (XRD; n = 69), and thin sections (n = 69) were used to develop a high-resolution integrated macrofacies and microfacies scheme. The four most volumetrically abundant facies include detrital-quartz-silt-bearing fine mudstone (facies 1), radiolarian-bearing calcareous fine mudstone (facies 2), detrital-quartz-silt- and shell-bearing calcareous fine mudstone (facies 3), and calcareous wackestone (facies 4). All four facies are volumetrically dominated by carbonate mud matrix (i.e., micrite) that represents either 1) original pelagic coccolithophore deposition modified by diagenesis, 2) transported carbonate mud (i.e., bottom currents like contour currents or sediment gravity flows), or 3) a combination of both. Outcrop observations, XRD mineralogic trends, and petrographic variations in grain composition between detrital quartz silt, radiolarian and microfossil to macrofossil content (mainly benthic foraminifera and bivalves) distinguish the four mudstone facies. The facies scheme indicates distinctly more heterogeneous and current-influenced sedimentation in the downdip sub-storm wave base than previously described in the Agrio and in carbonate-dominated basinal settings in general. A depositional model is proposed for further testing that may prove valuable towards re-evaluating basinal carbonate mudstone successions worldwide. Utilizing TOC, S2, and HI value cutoffs, this study defines five discrete stratigraphic packages in the Agrio Formation that have the highest source potential, collectively totaling ∼ 140 m thick. The novel integration of macrofacies and microfacies analysis, stratigraphy, and a geochemical analysis allow both depositional insights and the assessment of a potential source rock. The study adds to a growing body of literature on 1) carbonate ramp (or slope) to basinal processes and 2) facies models for organic-rich, carbonate-dominated mudstone successions that are unconventional hydrocarbon systems.