Abstract: As a common pollutant of nitrogen in groundwater, nitrate contamination has become a major concern worldwide. Baseflow, one of the dominant hydrological pathways for nitrate migration to streamflow, has been confirmed as a leading nitrate source for stream water where groundwater or subsurface flow contaminated heavily by nitrate. That is, sufficient improvements of water quality may not be attained without proper management for baseflow, even if non-point sources (NPS) pollutants discharged through surface runoff are being well managed. This article reviews the primary nitrate sources, the main factors affecting its transport, and the methodologies for baseflow nitrate estimation, to give some recommendations for future works, including: (1) giving sufficient consideration for the effects of climatological, morphological, and geological factors on baseflow recessions to obtain more reliable and accurate baseflow separation; (2) trying to solve calibration and validation problems for baseflow loads determining in storm flow period; (3) developing a simple and convenient algorithm with certain physics that can be used to separate baseflow NPS pollution from the total directly in different regions, for a reliable estimation of baseflow NPS pollution at larger scale (e.g., national scale); (4) improving groundwater quality simulation module of existing NPS pollution models to have a better simulation for biogeochemical processes in shallow aquifers; (5) taking integrated measures of "source control", "process interception" and "end remediation" to prevent and control NPS nitrate pollution effectively, not just only the strict control of nutrients loss from surface runoff.