The Johnson River Basin, located in Lake Clark National Park and Preserve, drains an area of 96 square miles. A private inholding in the upper part of the basin contains a gold deposit that may be developed in the future. To establish a natural baseline to compare potential effects on water quality if development were to occur, the upper part of the Johnson River Basin was studied from 1999 to 2001 as part of a cooperative study with the National Park Service. Two basic rock types occur within the drainage basin of the study: the Jurassic Talkeetna Formation of interbedded volcanic and volcaniclastic rocks, and the slightly younger plutonic rocks of the Aleutian-Alaska Ranges batholith. The Johnson River gold prospect reflects widespread, secondary mineralization and alteration of the Talkeetna Formation. Metals found at the prospect proper are: arsenic, cadmium, copper, gold, iron, lead, mercury, molybdenum, selenium, silver, and zinc. The Johnson River prospect is located in the East Fork Ore Creek Basin, a 0.5 square mile watershed that is a tributary to the Johnson River. Water quality data from this stream reflect the mineralization of the basin and the highest concentrations of several trace elements and major ions of the water column were found in this stream. Presently, pH in this stream is normal, indicating that there is sufficient buffering capacity. At the Johnson River streamgage, which drains approximately 25 mi2 including the East Fork Ore Creek, concentrations of these constituents are significantly lower, reflecting the runoff from Johnson Glacier and Double Glacier, which account for approximately 75 percent of the total discharge. Streambed concentrations of cadmium, lead, and zinc from East Fork Ore Creek and its receiving stream, Ore Creek, typically exceed concentrations where sediment dwelling organisms would be affected. Similar to the water column chemistry, concentrations of these elements are lower at the Johnson River streamgage, reflecting the fine sediment input from the glacier streams draining Johnson Glacier and Double Glacier. The amount of organic carbon present in the study area is relatively low and most sites indicate that some degree of toxicity is present even though these basins do not contain mineralized areas. Acid based accounting tests on rock samples in the study area indicate a neutralizing capacity in the Talkeetna Formation rocks. These results should be used with caution because similar tests were not done on rocks from narrow veins or faults that could have acid generating potential. In addition, based on field tests during the study, carbonate-bearing rocks in streambeds are armored by a carbonate-depleted shell and would not readily neutralize acidic water.