The calcium-based substrate, plants and microorganisms and their interactions in constructed wetlands (CWs) could affect the removal performance and transformation of fluoride (F-). CWs with limestone additive enhanced F- removal during the first 40 days. The results of scanning electron microscopy-energy dispersive spectrometer (SEM-EDS) and X-ray photoelectron spectroscopy (XPS) revealed the presence of Ca2+ precipitate components, and X-ray diffraction (XRD) demonstrated the formation of CaF2, Ca5(PO4)3F, and Ca3(PO4)2 precipitation, which all attributed to the synergetic effects of adsorption and co-precipitation. However, the F- removal efficiency of both CWs were diminishing step by step and reached as high as influent concentration around 50th day. The F- effluent concentration stabilized at 3.81 ± 0.02 mg/L and 3.72 ± 0.03 mg/L in calcium-based group and control group, respectively. The weak F- removal performance in plant-uprooted CWs confirmed that plants promoted the release of adsorbed F- and the dissolution of Ca5(PO4)3F by reducing overall pH value of CWs substrate whether with limestone additive or not. Furthermore, the lower relative abundance of fluoride-tolerant bacteria was observed in plant-uprooted CWs compared with planted CWs. This study had important implications for understanding the F- transformation in calcium-based CWs, and could be referenced by the application, design, and construction of constructed wetlands in fluoride-contaminated regions.