Groundwater contamination by agricultural fertilizers has become a major environmental concern due to the widespread use of nitrogen- and phosphorus-based inputs aimed at sustaining crop productivity. Excessive or poorly managed fertilizer applications contribute to nitrate accumulation in the unsaturated zone and elevated nitrate concentrations in groundwater, with potential implications for drinking water quality, ecosystem functioning, and human health. However, the magnitude of groundwater contamination is influenced by multiple interacting factors, including soil properties, hydrological conditions, climatic variability, and the legacy effects of historical fertilization practices. This review synthesizes current evidence regarding the relationships between fertilizer inputs and groundwater contamination dynamics. Particular emphasis is placed on nitrate leaching associated with nitrogen fertilization, the hydrological and soil factors controlling contaminant transport, and the effectiveness of mitigation strategies designed to reduce groundwater pollution. In addition, the review discusses the indirect implications of phosphorus and fertilizer-derived heavy metals for groundwater quality and highlights the importance of integrated nutrient management approaches. The available evidence indicates that groundwater quality responses to fertilizer use are highly context-dependent and may reflect both present and past agricultural practices. Improved fertilizer management, enhanced-efficiency products, optimized application timing, and policy interventions can substantially reduce contamination risks. Understanding these complex interactions is essential for developing agricultural systems capable of maintaining productivity while protecting groundwater resources.