Testudines are one of the best-represented taxonomic groups among the Paleogene taxa of the Duero Basin (Castile and Leon Autonomous Community, central Spain). Among them, Neochelys (Podocnemidide) and Allaeochelys (Carettochelyidae) are most abundant, allowing the population to be assessed for osteological anomalies. The abundance of postcranial remains of both taxa allows us to identify several individuals with potential anomalies, mostly in their shells. Some of them have already been described in previous studies, but most of them are still unpublished. The objective of this study is to analyze in detail the anomalous Neochelys and Allaeochelys remains. As a result, different categories of causal agents (such as bacteria, fungi, parasites, or trauma) have been identified as potential producers of the anomalies in these freshwater turtles. Information regarding the pathogenesis and healing stages of some of these anomalies is provided.