Abstract Discerning paleoclimate parameters in depositional systems of the continental interior is challenging because the system response and stratigraphic record of climate are controlled by tectonic processes and are mediated through landscape and hydrological evolution of fluvial lacustrine systems. Climate and tectonic signals cannot be deconvolved from stratigraphic patterns alone but require additional information or data sets that directly record climate or tectonic influence. The Carnian Los Rastros Formation in northwest Argentina provides an excellent case study that integrates an appropriate range of information in a system with strong climate and tectonic signals, being deposited in part during the Carnian Pluvial Episode and spanning the active rift phase of the Ischigualasto–Villa Unión Basin. We examined the stratigraphic and spatial patterns of carbon (C) and oxygen (O) stable isotopes in lacustrine carbonates from the Los Rastros Formation in multiple parts of the basin to constrain paleohydrological conditions and paleotemperatures. Practically all C and O isotope values are characterized by negative values: δ18Ocarb –11.6‰ and –15.7‰ (χ average –13.1‰; 1σ = 1.6) and δ13Ccarb –2.6‰ to –8.0‰ (χ average –5.1‰; 1σ = 2.1), reflecting the latitude, altitude, and continentality of the lake system and its vegetated and humid catchment area. Stratigraphic patterns of stable isotope data from two different localities (Cerro Bola North and Cerro Bola South) show a change from short water-residence time to long residence time and back to short residence time. This contrasts with sedimentologic, organic geochemical, and small-scale stratigraphic patterns that indicate an overfilled lake basin, which is expected to contain a completely open-hydrology isotopic signature. Paleotemperatures calculated from marginal lacustrine carbonates show a warm and quite variable paleothermal range consonant with their continental interior position and with Global Climate Models estimates for high paleolatitudes. Warmer paleotemperatures (linked to aridity, probably smaller lake size, and less thermal mass) precede the Carnian Pluvial Episode, whereas relatively cooler paleotemperatures coincide with the Carnian Pluvial Episode (linked to humidity, probably larger lake size, and more thermal mass). Carbon and oxygen stable isotope signatures integrated with sedimentologic and physiographic information allow us to propose that tectonics, specifically, half-graben tilting during the active synrift phase, dominated over climate effects as the cause of hydrological fluctuations of this system, even during the Carnian Pluvial Episode. Without appropriate stratigraphic-tectonic context, single-proxy reconstructions of continental-interior paleoclimate can be misleading. A robust interpretation of climate effects requires characterization of tectonic effects, geomorphology, paleohydrology, and sedimentary system responses.