Anisian Muschelkalk carbonates of the southern Germanic Basin containing silicified ooidal grainstone are interpreted as evidence of changing pH conditions triggered by increased bioproductivity (marine phytoplankton) and terrestrial input of plant debris during maximum flooding. Three distinct stages of calcite ooid replacement by silica were detected. Stage 1 reflects authigenic quartz development during the growth of the ooids, suggesting a change in the pH–temperature regime of the depositional environment. Stages 2 and 3 are found in silica-rich domains. The composition of silica-rich ooids shows significant Al2O3 and SrO but no FeO and MnO, indicating that late diagenetic alteration was minor. Silicified interparticle pore space is characterized by excellent preservation of marine prasinophytes; palynological slides show high abundance of terrestrial phytoclasts. The implications of our findings for basin dynamics reach from paleogeography to cyclostratigraphy and sequence stratigraphy, since changes in the seawater chemistry and sedimentary organic matter distribution reflect both the marine conditions as well as the hinterland. Basin interior changes might overprint the influence of the Tethys Ocean through the eastern and western gate areas. Stratigraphically, such changes might enhance marine flooding signals. Ongoing research needs to address the complex interaction between an intracratonic basin and an open-ocean system by comparing local and regional biotic and abiotic signals.