Nitrate is widely distributed in groundwater, posing an increasing threat to both water resources and human health. In this study, the treatment performance, removal mechanisms and environmental risks of sulfur-based constructed wetlands (CWs) for purifying nitrate-contaminated groundwater were investigated. Results showed that sulfur-based CWs could achieve the highest nitrate removal (95%). However, sulfate was largely produced as a by-product in sulfur-based CWs, which declined the nitrogen and phosphorus assimilation by plants. Metagenomic analysis indicated that autotrophs denitrifiers (e.g., Thiobacillus) were enriched, and the abundance of nitrate removal genes was enhanced in sulfur-based CWs. Additionally, sulfur cycle was formed in sulfur-based CWs, which explained the highest nitrate removal reasonably. This study provides comprehensive insights into the nitrate removal mechanisms in sulfur-based CWs and the associated environmental risks in purifying the polluted groundwater.