Aims: This study compared the chemical, physical and bacterial composition of circulated and stagnant dairy wastewaters. Methods and Results: Samples taken from circulated and stagnant wastewater lagoons, over a 1-year period, were analysed for 10 chemical (total N, NH3, NO3, NO2, Na, Ca, HCO3, Fe, P and K) and six physical (biological oxygen demand, chemical oxygen demand, dissolved solids, electrical conductivity, pH and sodium absorption ratio) parameters and were found to be similar. The 16S rDNA genes from the samples were amplified, cloned and BLAST analysed. In total, 996 stagnant and 1052 circulated wastewater derived sequences were obtained, comprising 294 and 362 operational taxonomic units (OTUs) from the circulated and stagnant wastewaters respectively. Coverage estimates of the OTUs identified were 72.1% for the stagnant, and 63.6% for the circulated wastewater libraries. The greatest difference between the two wastewaters was a c. sixfold greater number of sequences representative of the family Chromatiaceae in the circulated wastewater derived library and a c. fivefold greater number of sequences representative of the phylum Chloroflexi in the stagnant wastewater derived library. Conclusions: Circulation of dairy wastewater does not affect any of the chemical or physical parameters tested; however, circulation does alter the bacterial community structure. Significance and Impact of the Study: This study provides evidence that circulation of dairy wastewater promotes the growth of bacteria within the family Chromatiaceae and that stagnant systems promote the growth of the phylum Chloroflexi.