California's dairies are the largest confined animal industry in the state. A major portion of these dairies, which have an average herd size of nearly 1000 animal units, are located in low-relief valleys and basins. Large amounts of liquid manure are generated and stored in these dairies. In the semi-arid climate, liquid manure is frequently applied via flood or furrow irrigation to forage crops that are grown almost year-round. Little is known about the impact of manure management practices on water quality of the extensive alluvial aquifers underlying these basins. The objective of this work is to assess nitrate and salt leaching to shallow groundwater in a relatively vulnerable hydrogeologic region and to quantify the impact from individual sources on dairies. The complex array of potential point and nonpoint sources was divided into three major source areas representing farm management units: (1) manure water lagoons (ponds); (2) feedlot or exercise yard, dry manure, and feed storage areas (corrals); and (3) manure irrigated forage fields (fields). An extensive shallow groundwater-monitoring network (44 wells) was installed in five representative dairy operations in the northeastern San Joaquin Valley, CA. Water quality (electrical conductivity, nitrate-nitrogen, total Kjehldahl nitrogen) was observed over a 4-year period. Nitrate-N, reduced nitrogen and electrical conductivity (EC, salinity) were subject to large spatial and temporal variability. The range of observed nitrate-N and salinity levels was similar on all five dairies. Average shallow groundwater nitrate-N concentrations within the dairies were 64 mg/l compared to 24 mg/l in shallow wells immediately upgradient of these dairies. Average EC levels were 1.9 mS/cm within the dairies and 0.8 mS/cm immediately upgradient. Within the dairies, nitrate-N levels did not significantly vary across dairy management units. However, EC levels were significantly higher in corral and pond areas (2.3 mS/cm) than in field areas (1.6 mS/cm) indicating leaching from those management units. Pond leaching was further inferred from the presence of reduced nitrogen in three of four wells located immediately downgradient of pond berms. The estimated minimum average annual groundwater nitrate-N and salt loading from manure-treated forage fields were 280 and 4300 kg/ha, respectively. Leaching rates for ponds are estimated to be on the order of 0.8 m/year, at least locally. Since manure-treated fields represent by far the largest land area of the dairy, proper nutrient management will be a key to protecting groundwater quality in dairy regions overlying alluvial aquifers.