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This work provides new insights to assess the factors controlling carbonate deposition in the siliciclastic fluvial systems of rift basins. Sedimentological and stable-isotope data of microbialites and associated carbonate facies, along with regional geological information, are shown to reveal the influence of climate and tectonics on the occurrence and attributes of carbonate deposits in these settings. The Vega Formation - a 150m thick Lower Kimmeridgian siliciclastic fluvial sequence in Asturias Province (northern Spain) - constitutes a candidate for this approach. This unit includes varied facies (stromatolites; rudstones, packstones and wackestones containing oncoids, intraclasts, charophytes and shell bioclasts; marlstones and polygenic calcareous conglomerates) that formed in a low-gradient fluvial-lacustrine system consisting of shallow, low-sinuosity oncoid-bearing channels and pools within marshy areas, with sporadic coarse alluvial deposition. The sedimentological attributes indicate common erosion by channel overflow and rapid lateral changes of subenvironments caused by water-discharge variations. The carbonate fluvial-lacustrine system developed near uplifted marine Jurassic rocks. The occurrence of the system was conditioned by normal faults (active during the deposition of the unit) that favoured: (i) springs of HCO3-Ca-rich water from a Rhaetian-Sinemurian carbonate rock aquifer; and (ii) carbonate deposition in areas partially isolated from the adjacent siliciclastic fluvial system. The microbialite C-13 and O-18 values support deposition in a hydrologically open system, fed by ambient-temperature meteoric water, with riparian vegetation. Three types of lamination in the stromatolites and oncoids reflect distinct morphological types of cyanobacterial communities. The textural pattern of lamination parallels C-13 and (18)Ochanges, suggesting short-term cycles of precipitation and temperature. A moderately to strongly contrasted seasonal and/or pluriannual precipitation regime is inferred from the cyclic C-13 pattern of the lamination and from the discontinuous and asymmetrical growth of oncoids. Thus, the isotopic and sedimentological attributes of the carbonate deposits were linked to short-term climate changes associated with semi-arid conditions, consistent with the studied climatic zone.