The palynological information of the Paso Aguiar Formation (Paraná Basin, Uruguay) is scarce, and the overlying Yaguarí Formation has been hitherto considered as barren. In this study, the palynology and palynofacies of 17 samples recovered from borehole DINAMIGE 943 “Estancia El Águila”, drilled in the Cerro Largo Department (northeastern Uruguay), are analyzed. Palynological assemblages are dominated by striate bisaccate pollen grains, mainly those assigned to the genera Staurosaccites and Lueckisporites, and subordinated apiculate monolete and cingulizonate-cavate spores, essentially represented by Thymospora and Lundbladispora, Gondisporites, and Spelaeotriletes, respectively. The assemblages also include non-taeniate bisaccate and plicate-colpate pollen grains, laevigate and apiculate trilete spores, and algae. Moreover, laevigate monolete spores, non-taeniate and taeniate monosaccate pollen grains, and acritarchs are present in low quantities. The diverse palynoassemblages constitute evidence of a source palaeoflora primarily composed of gymnosperms, with important contributions from glossopterids and conifers. This is complemented by sub-dominant ferns and lycophytes, implying seasonally warmer and humid climates. The palynofacies analysis suggests marine depositional environments with terrestrial inputs related to fluvio-deltaic discharges. Proximal-distal variations are inferred for the lower and middle levels of the Paso Aguiar Formation, while high-energy proximal marine settings with variable redox conditions are deduced for the upper Paso Aguiar Formation and the lower Yaguarí Formation. The abundance of spores recorded is noteworthy, particularly when considering the environmental interpretations for these units. However, the influence of differences in preservation among palynomorphs cannot be entirely ruled out. The assemblages are assigned to the Striatoabieites anaverrucosus-Staurosaccites cordubensis Zone of the Paraná Basin in Uruguay. Nevertheless, obtaining additional data from the studied geological units is crucial to enhance and fine-tune the existing palynostratigraphic framework. Considering the radiometric ages available for the Paraná Basin, along with the ages proposed for comparable biozones in the region and assemblages from correlative units in Brazil, a late Cisuralian–late Guadalupian (Kungurian to Capitanian) age is suggested for the studied section.