Aims: This study examined the impact of pipe materials and introduced Legionella pneumophila on downstream Leg. pneumophila colonization and microbial community structures under conditions of low flow and low chlorine residual. Methods and Results: CDC biofilm (TM) reactors containing either unplasticized polyvinylchloride (uPVC) or copper (Cu) coupons were used to develop mature biofilms on Norprene (TM) tubing effluent lines to simulate possible in-premise biofilm conditions. The microbial communities were characterized through 16S and 18S rRNA gene clone libraries and Leg. pneumophila colonization was determined via specific qPCR assays. The Cu significantly decreased downstream microbial diversity, approximately halved bacterial and eukaryotic abundance, with some groups only detected in uPVC-reactor tubing biofilms. However, some probable amoeba-resisting bacteria (ARB) like Mycobacterium spp. and Rhodobacteraceae were significantly more abundant in the Cu than uPVC-reactor tubing biofilms. In particular, Leg. pneumophila only persisted (postinoculation) within the Cu-reactor tubing biofilms, and the controlled low chlorine residue and water flow conditions led to a general high abundance of possible free-living protozoa in all tubing biofilms. The higher relative abundance of ARB-like sequences from Cu-coupons vs uPVC may have been promoted by amoebal selection and subsequent ARB protection from Cu inhibitory effects. Conclusions: Copper pipe and low flow conditions had significant impact on downstream biofilm microbial structures (on plastic pipe) and the ability for Leg. pneumophila colonization post an introduction event. Significance and Impact of the Study: This is the first report that compares the effects of copper and uPVC materials on downstream biofilm communities grown on a third (Norprene (TM)) surface material. The downstream biofilms contained a high abundance of free-living amoebae and ARB, which may have been driven by a lack of residual disinfectant and periodic stagnant conditions. Given the prevalence of Cu-piping in buildings, there may be increased risk from drinking water exposures to ARB following growth on pipe/fixture biofilms within premise drinking water systems.