The development and utilization of unconventional water resources has become a strategy to alleviate the agricultural water crisis in many countries and regions. To understand the research progress, hot spots, and future trends in the field of unconventional water agricultural irrigation (UWAI), this paper systematically analyzes 6738 publications based on the core database of Web of Science 1990–2023 using the scientific bibliometric analysis software CiteSpace, VOSviewer, and Scimago Graphica. The results showed that the research on UWAI is always rapidly developing. Soil science, crop science, and bioengineering are the main disciplines involved. Most research on WUAI has occurred in China and the United States. Countries with higher levels of development tend to have more influence. Collaboration among authors is fragmented, and collaboration between authors and states needs to be strengthened. Through keyword analysis, the research hotspots are summarized as follows: (1) The effects of traditional and emerging pollutants brought by unconventional water irrigation on soil physicochemical properties, crop growth, and groundwater quality; (2) the health threats caused by pollutants entering the food chain and groundwater; (3) unconventional water utilization technologies, including rainwater harvesting agriculture, precision agriculture, and urban agriculture. Future research hotspots will focus on the mechanisms of pollutant solute transport and transformation in the water–soil–crop system under non-conventional water irrigation conditions and crop physiological responses. We suggest that the research on traditional and emerging pollutants in unconventional water should be strengthened in the future, and the risk control system of unconventional water irrigation should be improved. International cooperation should be strengthened, especially with poor countries in arid regions, to promote the formation of unified international standards and guidelines for non-conventional water irrigation in agriculture.