Anthropogenic threats such as water infrastructure, land-use changes, overexploitation of fishes and other biological resources, invasive species and climate change present formidable challenges to freshwater biodiversity. Historically, management of fish and fishery species has largely been based on studies of population- and community-level dynamics; however, the emerging field of conservation physiology promotes the assessment of individual fish health as a key management tool. Fish health is highly sensitive to environmental disturbances and is also a fundamental driver of fitness, with implications for population dynamics such as recruitment and resilience. However, the mechanistic links between particular anthropogenic disturbances and changes in fish health, or impact pathways, are diverse and complex. The diversity of ways in which fish health can be measured also presents a challenge for researchers deciding on methods to employ in studies seeking to understand the impact of these threats. In this review, we aim to provide an understanding of the pathway through which anthropogenic threats in freshwater ecosystems impact fish health and the ways in which fish health components impacted by anthropogenic threats can be assessed. We employ a quantitative systematic approach to a corpus of papers related to fish health in freshwater and utilize a framework that summarizes the impact pathway of anthropogenic threats through environmental alterations and impact mechanisms that cause a response in fish health. We found that land-use changes were the most prolific anthropogenic threat, with a range of different health metrics being suitable for assessing the impact of this threat. Almost all anthropogenic threats impacted fish health through two or more impact pathways. A robust understanding of the impact pathways of anthropogenic threats and the fish health metrics that are sensitive to these threats is crucial for fisheries managers seeking to undertake targeted management of freshwater ecosystems.