Ground water was sampled from wells completed in the Gallup, Dakota, and Morrison aquifers in the San Juan Basin, New Mexico, to examine controls on solute concentrations. Samples were collected from 38 wells primarily from the Morrison aquifer (25 wells) in the northwestern part of the basin. A series of samples was collected along ground-water flow paths; dissolved constituents varied horizontally and vertically. The understanding of the flow system changed as a result of the geochemical analyses. The conceptual model of the flow system in the Morrison aquifer prior to the study reported here assumed the Westwater Canyon Member of the Morrison aquifer as the only significant regional aquifer; flow was assumed to be two dimensional; and vertical leakage was assumed to be negligible. The geochemical results indicate that the Westwater Canyon Member is not the only major water-yielding zone and that the flow system is three dimensional. The data presented in this report suggest an upward component of flow into the Morrison aquifer. The entire section above and below the Morrison aquifer appears to be controlled by a three-dimensional flow regime where saline brine leaks near the San Juan River discharge area. Predominant ions in the Gallup aquifer were calcium bicarbonate in recharge areas and sodium sulfate in discharge areas. In the Dakota aquifer, predominant ions were sodium bicarbonate and sodium sulfate. Water in the Morrison aquifer was predominantly sodium bicarbonate in the recharge area, changing to sodium sulfate downgradient. Chemical and radioisotopic data indicate that water from overlying and underlying units mixes with recharge water in the Morrison aquifer. Recharge water contained a large ratio of chlorine-36 to chlorine and a small ratio of bromide to chloride. Approximately 10 miles downgradient, samples from four wells completed in the Morrison aquifer were considerably different in composition compared to recharge samples. Oxygen stable isotopes decreased by 2.8 per mil and deuterium decreased 26 per mil, relative to recharge. Carbon-14 radioisotope activities were not detectable. Chloride-36 radioisotope ratios were small and bromide to chloride concentration ratios were large. These results suggest two potentially viable processes: ion filtration or trapping of ancient dilute water recharged under a humid climate. For water samples near the San Juan River, pH decreased to about 8.0, chloride concentrations increased to more than 100 milligrams per liter, and ratios of chlorine-36 to chlorine and bromide to chloride were small. Leakage of deep basin brine into the fresher water of the Morrison aquifer appears to control ion concentrations.