Fossils from the Jurassic succession of the Neuquén Basin (Argentina) were analysed for their stable isotope (δ13C, δ18O) and elemental (Mg/Ca, Sr/Ca) composition. Mg/Ca ratios point to comparatively stable temperature conditions from the Bajocian to Early Oxfordian and during the Tithonian, but do not allow a reliable reconstruction of absolute water temperatures. Sr/Ca ratios follow the general global pattern indicating water exchange between the basin and the open ocean. The δ18O values can be translated into water temperatures between 20 to 25 °C for most of the studied intervals with possible shorter cold spells in the Late Pliensbachian, Bajocian, and Late Tithonian. However, precise temperature reconstructions are complicated by bivalve shells from the northern/central part of the basin pointing to local fluctuations in the δ18O values of seawater. Potential reasons for these variations are discussed, but it seems most likely that they are caused by phases of enhanced freshwater input leading to meso- to brachyhaline conditions in the northern study areas. The present article therefore exemplifies the particular challenges for temperature reconstructions in marginal seas and highlights the opportunities of combining different geochemical proxies to disentangle the influence of different environmental parameters.