Groundwater of the unconfined Chalk aquifer in Champagne-Ardenne (NE France) is contaminated by perchlorate (⁠$ClO4−$⁠), a persistent water-soluble anion. The Chalk aquifer is a crucial water resource of the region, with complex hydraulic properties. The presence of $ClO4−$ is of concern due to its potential adverse human health effects. In France, three sources of $ClO4−$ contamination are suspected: industrial, military and agricultural. Both a comprehensive understanding of hydrogeological characteristics of the aquifer, and a sound knowledge of sources and behaviour of $ClO4−$ in groundwater are required to allow the sustainable use of this groundwater resource. From data acquired during hydrogeological, geochemical, isotopic (⁠$ClO4−$⁠) and groundwater age (CFCs and SF₆) studies, and historical investigations in a study area located east of Reims, a conceptual model of Chalk aquifer function and $ClO4−$ transfer has been established. High spatio-temporal heterogeneities in the unconfined Chalk aquifer are discussed. Different correlations between $ClO4−$⁠, major ions and groundwater-level fluctuations are shown and interpreted, highlighting main factors governing the Chalk groundwater geochemistry and $ClO4−$ transfer mechanisms, including water-level fluctuation, groundwater residence time, thickness of the unsaturated zone, superficial formations, distribution of fissure networks, aquifer–river relationships, origin and location of $ClO4−$ in soil and human activity.