About 15% of couples worldwide are affected by infertility, with the male factor responsible for approximately 50% of reproductive failures. Male fertility can be influenced by various factors, including an unhealthy lifestyle and diet, often associated with oxidative stress. These changes are frequently the reason for spermatozoan dysfunction, malformations, and lowered count. However, sometimes even with proper semen parameters, fertilization does not occur, and this is referred to as idiopathic infertility. Of particular importance may be molecules contained in the spermatozoan membrane or seminal plasma, such as polyunsaturated fatty acids, including omega-3 (docosahexaenoic and eicosapentaenoic acids) and omega-6 (arachidonic acid) fatty acids and their derivatives (prostaglandins, leukotrienes, thromboxanes, endocannabinoids, isoprostanes), which are vulnerable to the effects of oxidative stress. In the present review, we discuss the influence of these molecules on human male reproductive health and its possible causes, including disrupted oxidative–antioxidative balance. The review also discusses the potential use of these molecules in the diagnostics and treatment of male infertility, with a particular focus on the innovative approach to isoprostanes as biomarkers for male infertility. Given the high occurrence of idiopathic male infertility, there is a need to explore new solutions for the diagnosis and treatment of this condition.