Karst aquifers are extremely vulnerable to pollution, including from nitrate. This research advances a systematic evaluation of water quality dynamics and processes in a relatively pristine karst flow system impacted by seasonal tourism, in particular migration and transformation of nitrate. Water samples from the Shuifang Spring basin (Jinfoshan Karst World Heritage Site, Chongqing, China) were collected for analysis of ion concentrations and dual nitrate isotopes. The principal sampling sites included untreated tap water from the Jinfoshan Holiday Hotel (JHH), JHH septic system effluent, discharged effluent at Sinkhole #1, and groundwater at Shuifang Spring (SFS, the resurgence of the basin). Sampling from April 2017 through April 2018 showed that higher nitrate concentrations were observed at SFS during busy tourist seasons that occurred in the summer drought and winter dry seasons. Between the septic system and SFS, nitrate was diluted by rainwater and infiltration from the matrix regions of the karst aquifer in the wet season. The MixSIAR model quantitatively revealed that nitrate from manure and sewage (M&S), soil organic nitrogen (SON) and atmospheric precipitation (AP) contributed roughly 55%, 41% and 4% on average, respectively. The mixture of effluent and oxygen-rich tap water from the JHH underwent nitrification at the septic system and Sinkhole #1. After the nitrification and decomposition of organic matter with oxygen consumption in the effluent, denitrification was the dominant response to nitrate attenuation in the effluent of Sinkhole #1 during peak tourism periods. The septic effluent sinking into the aquifer deteriorated the groundwater quality, which was controlled by nitrification in the summer drought and winter dry seasons. In contrast, microorganisms in groundwater assimilated nitrate from effluent in the wet season. Because of the relatively pristine ambient background conditions and seasonal tourism, these results can inform interpretation of background and impacted nitrogen processes in a range of karst settings.Copyright © 2020 Elsevier B.V. All rights reserved.