Controversy has developed over the last few years as to whether or not water nipple lines or water troughs are more appropriate for Pekin ducks in grow-out commercial barns. We hypothesized that water troughs would show improved duck body conditions and environmental quality compared to pin-metered water lines. To test this hypothesis, we housed ducks in two barns, one with water lines and one with water troughs. Water troughs were constructed to meet RSPCA guidelines for number and density of ducks and with recently described verandas. Ducks were divided into 4 pens per barn (n = 1000 ducks/pen). The study was then repeated (n = 8 pens per water source). Ducks were scored for physical traits and assessed for microbial cecal content changes through 16S amplicon sequencing. Water samples were assessed for culturable microbial loads and for microbial community through 16S amplicon sequencing.