Groundwater is a major source of water, meeting the domestic water needs of more than 70% of Africa's population. Although prized for its relatively good quality compared with surface water, groundwater is increasingly subjected to multiple sources of pollution. Long thought to be the solution to increasing agricultural production and achieving food self-sufficiency, agricultural inputs are now being pointed out in Burkina Faso as a major source of water pollution. However, few studies exist showing the contribution of agricultural inputs to groundwater pollution. The aim of this study is to show the impact of the use of agricultural inputs on groundwater quality: the case of the Boulbi valley rice-growing area in Burkina Faso, West Africa. Soil properties were measured using a double-ring infiltrometer and Harmonized World Soil Database. Groundwater recharge was assessed by Thornthwaite’s equation. The DRASTIC, GOD and SI methods were applied to map the valley’s vulnerability. Fertilizers and phytochemicals were recorded by surveys. A sampling of surface and groundwater was done in 32 locations and the chemical characteristics (pH, EC, NO<sup>3-</sup>, SO<sub>4</sub><sup>2-</sup>, PO<sub>4</sub><sup>2-</sup> and K<sup>+</sup>) confronted with the vulnerability indices. Results show that the soils were predominantly clay (41%), silt (37%) and silty sand (22%). Twenty types of phytochemicals were used, among which 35% were composed of the controversial glyphosate (denounced as carcinogenic) and 30% made with paraquat chloride also accused of being responsible for several self-poisoning. All the three methods pointed to a low vulnerability risk, partly because of the purification role of clay. The average pH is 8.2 ± 0.4, explaining the low-rice yield (<4.0 tons/ha), in spite of fertilizer use. Although the risk assessment rendered non-alarming situation, preventive measures about health and environment need to be taken.