Male infertility is one of the many problems currently faced by science and medicine. Despite intensive research in this area conducted in recent years, the reasons for the lack of the desired pregnancy are often unrecognized. The current standards and general recommendations, including the World Health Organization (WHO) guidelines for diagnostic testing of male reproductive organs and sperm quality analysis, seem to be insufficient. Hence, it has been postulated for years that it is necessary to search for and identify new, unknown factors that significantly affect male fertility, and to define modern indicators/biomarkers that would enable precise determination of male reproductive potential. Among the many interesting recently published data, the information on the identification and expression analysis of aquaporins (AQPs) in the male reproductive system and metabolomic semen analysis is of particular interest. In this review, we will try to solve the question whether AQPs and metabolomic sperm analysis can be the answer to the current needs and whether their measurements may become a useful parameter in the future for determining male reproductive potential.