The triazine herbicide atrazine easily leaches with water through soil layers into groundwater, where it is persistent. Its behavior during short-term transport is poorly understood, and there is no in situ remediation method for it. The aim of this study was to investigate whether water circulation, or circulation combined with bioaugmentation (Pseudomonas sp. ADP, or four isolates from atrazine-contaminated sediments) alone or with biostimulation (Na-citrate), could enhance atrazine dissipation in subsurface sediment–water systems. Atrazine concentrations (100 mg L−1) in the liquid phase of sediment slurries and in the circulating water of sediment columns were followed for 10 days. Atrazine was rapidly degraded to 53–64 mg L−1 in the slurries, and further to 10–18 mg L−1 in the circulating water, by the inherent microbes of sediments collected from 13.6 m in an atrazine-contaminated aquifer. Bioaugmentation without or with biostimulation had minor effects on atrazine degradation. The microbial number simultaneously increased in the slurries from 1.0 × 103 to 0.8–1.0 × 108 cfu mL−1, and in the circulating water from 0.1–1.0 × 102 to 0.24–8.8 × 104 cfu mL−1. In sediments without added atrazine, the cultivable microbial numbers remained low at 0.82–8.0 × 104 cfu mL−1 in the slurries, and at 0.1–2.8 × 103 cfu mL−1 in the circulating water. The cultivated microorganisms belonged to the nine genera Acinetobacter, Burkholderia, Methylobacterium, Pseudomonas, Rhodococcus, Sphingomonas, Streptomyces, Variovorax and Williamsia; i.e., biodiversity was low. Water flow through the sediments released adsorbed and complex-bound atrazine for microbial degradation, though the residual concentration of 10–64 mg L−1 was high and could contaminate large groundwater volumes from a point source, e.g., during heavy rain or flooding.