Conditions and changing capacity. Production intensification has limited the capacity of agroecosystems to provide clean freshwater, often significantly. Both irrigated and rainfed agriculture can threaten downstream water quality by leaching fertilizers, pesticides, and manure into groundwater or surface water. Irrigated agriculture also risks pollution associated with water use, especially waterlogging and salinization, which decreases productivity. Salinization is estimated to reduce farm income by US$11 billion each year worldwide.

Data quality. No globally consistent indicators of water quality, as it relates to agriculture, exist. The quantity of nutrients---nitrogen and phosphorus---in water can be a good indicator of pollution from excess fertilizers and animal manure but are often difficult to separate from human effluent effects. Pesticides in water are specific indicators of agricultural pollution but are costly to measure. Data on suspended solids form soil erosion are also scarce and difficult to interpret.