The concentration of arsenic (As), considered a toxic and carcinogenic metalloid, in agricultural soils has become a global challenge. Sources of arsenic in soils can be both anthropogenic and natural. Contaminated water is used for the irrigation of crops and vegetables, and therefore it is the main pathway for arsenic to enter the human food chain, creating a potential health risk. This study evaluated the concentrations of arsenic in agricultural soils in the rural parish of Papallacta, located 67 km east of the city of Quito, Northeastern Ecuador, and constitutes an analysis of the problem of arsenic in agricultural soils. Shallow groundwater and geothermal water discharges laced with arsenic are frequently used for irrigation and have raised the level of arsenic in agricultural soils. This work is focused on evaluating the environmental quality and contamination of agricultural soils through environmental quality indices such as geo-accumulation index, enrichment, and contamination factor. The average arsenic levels in the agricultural soils of the four studied areas fluctuate between 20.4 and 43.0 mg kg−1, while in the sediments of the Papallacta Lake, higher values were found in the range between 16.8 and 102.4 mg kg−1; all of which exceed the permissible limit by the Ecuadorian Environmental Legislation for agricultural use (12 mg kg−1). The results of the study in the five studied sites of the Papallacta civil parish indicate low to moderate levels of arsenic enrichment, soils enriched by bedrock, and moderate to considerable contamination.