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<p><span>Stromatolitic carbonates were formed in ancient microbial mats, and, thus, provide unique geochemical archives to reconstruct palaeo-environments in which microbial life thrived and evolved. In this study, we report the first geochemical data of Miocene stromatolites from the Oberpullendorf Basin (Austria) that were formed during the Badenian salinity crisis at the north-western coast of the Paratethys Sea. The combined approach of trace element data obtained by quadrupol ICP-MS with C-O isotopes of individual stromatolite laminae is used to reconstruct short-term variations of palaeo-environmental conditions in microbial habitats of the Oberpullendorf Basin.</span></p><p><span>Stromatolitic carbonates in the lower stromatolite units show negative δ<sup>13</sup>C<sub>carb</sub> values and typical shale-normalized seawater-like rare earths and yttrium (REY<sub>SN</sub>) patterns with positive La<sub>SN</sub>, Gd<sub>SN</sub> anomalies, super-chondritic Y/Ho ratios, and heavy REY<sub>SN</sub> enrichments to light REY<sub>SN</sub>, indicating an open marine-dominated depositional setting. Stratigraphic upwards, stromatolitic carbonates show suppressed seawater-like REY<sub>SN</sub> signatures and increasing δ<sup>13</sup>C<sub>carb</sub> values that argue for the development of a restricted environment. Seawater-like REY<sub>SN</sub> patterns and homogenously distributed negative δ<sup>13</sup>C<sub>carb</sub> values in the stratigraphic uppermost part resemble the transition to fully marine environmental conditions again. Enrichment factors of bio-essential elements (Fe, Mn, Co, Zn, Mo, W) reflect sufficient element availability during marine conditions but limitation during the development of the (semi)closed lagoon.</span></p><p><span>We show that combined REY, C isotopes, and enrichment factors of bio-essential elements bear the unique potential to reconstruct temporal changes in paleo-environments and determine the availability of bio-essential elements in microbial habitats. This approach provides the groundwork for a better understanding of the evolution and development of microbial metabolisms under severely different atmospheric-hydrospheric on planet Earth and beyond.</span></p>