The effect of climate variability on estuarine water environments was assessed in two systems of the Bay of Biscay, the estuaries of Bilbao and Urdaibai, with contrasting morphology, hydrodynamic features and anthropogenic influence. To that purpose, the main time scales of variability in relevant environmental factors were established along spatial salinity gradients and, using a combination of multivariate and regression analyses, the contribution of each factor to the total variability, as well as the influence of climate factors in the seasonal and inter-annual estuarine environment variations were assessed. The major seasonal modes of variability in the water environments of both estuaries were accounted for by water temperature together with salinity stratification and/or chlorophyll