The origin of limestone–marl alternations (LMA) and their diagenesis is still lively debated. The most disputed question is whether original variations in sediment input control the differentiation of the precursor sediment into limestone and marl, or if a LMA can form without compositional differences in the precursor sediment. The Miocene brackish-water deposits (Rüssingen Formation) from the Mainz–Weisenau quarry in central Germany offer the opportunity to tackle this question. They are developed as a monospecific alternation of planar beds of moderately and poorly lithified sands of aragonitic Hydrobia snails, corresponding to “limestones” and “marls” in LMA, respectively. XRD analyses and the monospecific composition reveal only minor to no changes in sedimentary input and allow comparison of the preservation of Hydrobia in both lithologies. The differential preservation of the aragonitic fossils in lithified and less lithified layers is documented in thin-sections. CaCO3 contents are high throughout the measured section. However, XRD analyses revealed high amounts of aragonite and low amounts of calcite in less lithified beds, and the opposite in lithified beds in which calcite is the main mineral phase. Mg-calcite is abundant in both lithologies. Although the less lithified beds have experienced significant loss of aragonite by dissolution, they still mainly contain aragonite since the precursor sediment contained only aragonitic shells and Mg-calcite crusts. The relative amount of aragonite is higher than in the more lithified beds because the lithified beds imported the dissolved aragonite, which precipitated as calcite cements. This shifted the aragonite–calcite ratio to higher values in the less lithified beds than in the more lithified beds, although it is counterintuitive at first sight. This is supported by thin-section analyses and point counting, revealing moderate to good preservation of Hydrobia or their replacement by calcite spar in lithified beds, but intense dissolution of aragonite in less lithified beds. The aragonite–calcite ratio and the differential preservation of Hydrobia fit the model of differential diagenesis in “classical” LMAs, which assumes early diagenetic aragonite dissolution in marls and reprecipitation as calcite cement in limestones. It is concluded that the studied succession—although an endmember of LMA—was differentiated into lithified and unlithified beds by incomplete differential diagenesis while minor primary differences are not reflected in the change in lithology. The results suggest that the differentiation of a homogeneous precursor sediment into a LMA is possible and caution should be exercised using lithological change or proxies which are potentially altered by CaCO3 redistribution for cyclostratigraphic analyses.