Lake Junín resides at ~4100 meters above sea level on the Junín 'altiplano', an intermontane glacial basin between the Eastern and Western Cordilleras of the Peruvian Andes. During the dry season from June to August, this watershed is a crucial source of water for hydroelectric power, potable water, and agricultural irrigation in the region. This study presents the results of biogeochemical and stable isotopic datasets of key bioactive elements and major ions dissolved in lakes, streams, rivers, and springs within the Lake Junín watershed to further evaluate the controls over their chemical composition. An analysis of major cation and anion geochemistry is consistent with previous reports that all waters in the watershed are Ca-HCO3 type and reflect the dissolution of carbonate and alumino-silicate minerals. However, down-valley transects of four major input streams on the eastern side of the lake were analyzed, and suggest that the biogeochemical cycles controlling stream geochemistry are more complicated and require further analysis. The stable isotope ratios of oxygen and hydrogen show that all waters in the basin plot below the local meteoric water line of precipitation (LMWL) but surficial input streams and rivers are considerably closer to the LMWL than the lake itself. This study also presents the stable isotopic analyses of carbon in dissolved inorganic carbon (DIC), dissolved organic carbon (DOC), and particulate organic carbon (POC) to investigate the sources and complex processes controlling carbon in these waters. In addition, this study presents the results of heavy metal concentration analysis for water within the Lake Junín and neighboring Cerro de Pasco regions.