Pond-ditch circulation systems (PDCSs) were proved to be an appropriate operation selection in rural wastewater remediation. However, the biological dephosphorization process has not been investigated and quantified in PDCSs. In this study, PDCSs exhibited higher total phosphorus (TP) removal efficiencies (77.8%-97.4%). The activities of polyphosphate kinase (PPK) and exopolyphosphatase (PPX) tightly associated with phosphorus biological removal ranged from 0.356 to 11.844mumol hydroxamic acid min-1mg-1 protein, and 0.008 to 0.446mumol p-nitrophenol min-1mg-1 protein, respectively. Both PPK and PPX in PDCSs increased with time, peaked at day 30, and then declined, and were negatively correlated with sediment total phosphorus (STP), sediment inorganic phosphorus (SIP), P bound to Al/Fe/Mn oxides and hydroxides (NaOH-P), P associated with Ca (HCl-P), and organic matter (OM) (p<0.05). Results of high-throughput sequencing suggested that Bacillus (0.46%-19.77%) and Clostridium (0.40%-21.0%) genus might be the predominant groups in phosphorus aerobic biological absorption; while Geobacter (0.15%-4.74%) and Arthrobacter (0.03%-4.01%) genus dominated in anaerobic biological process. The RDA results showed that compared to the ditch, temperature (W-temp), TP, dissolved oxygen (DO), NaOH-P, and OM had stronger effects on microbial community structures in two ponds at day 30 than those at days 14 and 60. Path analysis further indicated that STP could impact PPK and PPX activities in PDCSs both directly and indirectly via altering the relative abundances of bacteria taxa. We found that the indirect effects of W-temp, DO, and OM on PPK and PPX activities mediated through modulating the relative abundances of bacteria taxa and STP. Our findings provide evidences that biological dephosphorization process in PDCSs are jointly modulated by environmental factors and microbial communities. The less-studied W-temp, DO, STP, and OM modulating the relative abundances of bacteria taxa was an existing but previously underestimated indirect pathway influencing on biological dephosphorization process in PDCSs.