This paper presents the impact of livestock activities and geochemical processes on the water quality of a fractured volcanic rock aquifer in the Lake Çıldır watershed, located at the northeastern part of Turkey. The existence of a high livestock population and animal grazing activities in meadow and pasturelands of the watershed during the short summer period poses serious stress on both surface and groundwater resources being the only drinking water supply for the local communities. Therefore, understanding the effect of grazing and livestock breeding activities occurring in the recharge areas of the fractured volcanic rock aquifer is vital to take precautions in order to protect limited water supplies at the watershed and vulnerable lake ecosystem as well. The mean nitrate content of the groundwater was measured at 6.4 ± 6.6 (std. dev) mg/L in the wet (before grazing) period and 7.1 ± 5.9 mg/L in the dry (after grazing) period. Despite low nitrate concentration levels of groundwater, microbial contamination was observed in the spring waters at alarming levels especially after the animal grazing activities. 56%, 26%, and 11% of the groundwater samples showed bacterial contamination in terms of total coliform, fecal coliform, and fecal streptococci contents, respectively, prior to grazing activity, while in pursuit of intense livestock grazing at highland, these microbial indicators have been increased to 92%, 85%, and 77% in the dry period. A significant increase observed in fecal contamination indicates the negative impact of livestock activities on groundwater quality. Al (200–638 µg/L) and Fe (66–218 µg/L) enrichments locally observed in groundwater were related to advanced argillic alteration (kaolinization) and hematization zones in pyroclastic rocks.