The aim of this paper is to define the constraints by geology, climate, and eustasy on the freshwater fish fossil record through a qualitative analysis. The impact of these factors on the access to and knowledge of the freshwater fish fossil record is also evoked. The focus is on Afro-Arabia for the last several 100 million years, which corresponds with the rise and diversification of the modern fish fauna on the continent. After a review of the main environmental changes recorded in Afro-Arabia through this time span, I briefly present the history of fish fossil record and the distribution of the associated fossiliferous sites. Then, effects of environmental factors on the freshwater fish fossil record are described and discussed through case studies. Depending on the size of the drainage system, the fossil taxonomic richness varies notably in relation with the hydrodynamism of the environment. Second, freshwater fish outcrops are associated with an increase in accommodation in all case studies. Moreover, environmental factors delimit our knowledge of the fossil record. To increase this knowledge, we have to prospect previously neglected areas but we also may give more attention to small fraction size fossils and to isolated bones.