Stratigraphic and sedimentologic analyses and geochemical data from the middle and late Miocene record in the southwestern-central sector of the Ebro Basin have allowed the evolution of its Neogene final fill stage to be characterized and its controlling factors to be discerned. The focus of these analyses was the distinct depositional environments that occurred over time (tecto-sedimentary units T6, T7, and T8). Twelve main associations of lacustrine, palustrine, fluvial, and alluvial facies revealed that the sedimentary processes leading to the formation of the units occurred in different environments in units T6 and T7 (middle and late Aragonian, i.e., Langhian–Serravallian) and in unit T8 (Vallesian–Turolian?, i.e., Tortonian). The depositional environments of units T6 and T7 encompassed a closed, shallow carbonate lake system with wide palustrine fringes. The lake was fed by small sandy and gravelly channels flowing from the southwest (Iberian Range) and a sandy fluvial system from the north (Pyrenees). Inputs were also received from a southeastward-flowing axial fluvial system (AS). The mouths of these systems commonly formed small deltaic sandy lobes on the northern lake margins. The evolution of unit T6 and in particular that of unit T7 was greatly influenced by Pyrenean tectonics. The depositional environments of unit T8 included the occurrence of the AS, but this system was soon replaced by an open, shallow carbonate lake surrounded by wide and shallow oncoid-bearing channels and palustrine tufaceous areas on its west-southwest margin. Distinct depositional events from the south and west, which involved intra-T8 erosion, resulted in minor coarse alluvial deposits. The carbonate system of unit T8 occurred in an open depression created after local erosion of the pre-T8 deposits and subsequent northward shifting of the AS since early deposition of unit T8, the origin of which was related to late contractile deformation in the northwestern Iberian Range. Bicarbonate- and calcium-rich water from the Mesozoic carbonate rocks in the Iberian Range fed the T8 system. Sedimentologic, δ13C, δ18O, and trace-element data support the change from closed to open drainage, and strongly suggest a general climate trend toward wetter and cooler conditions, which is consistent with the middle–late Miocene climate evolution of other European regions. Despite the general timing coincidence between unit T8 deposition and the opening process of the Ebro Basin, the attributes of the T8 deposits are inconclusive to support the previous hypothesis that the fluvial–lacustrine–palustrine system could be directly connected to the emptying drainage of the basin into the Mediterranean Sea. Instead, the results of this study demonstrate the combined influence of tectonics and climate on the evolution of the final fill stage of this part of the Ebro Basin. These results may be useful for assessing the influence of such allocyclic factors on the sedimentologic, hydrologic, and geochemical evolution of other intermontane lake basins.