Water conservation efforts have led to decreased water flow in buildings. Without resizing pipes and storage tanks, water retention time (WRT) increases, which may support opportunistic pathogen (OP) growth. Decreasing pipe diameters would allow lower flow volumes without increasing WRT. However, such alterations have other implications for bacterial regrowth and exposure to OPs, including increased surface area to volume ratios and altered shear velocities for mobilization of both sediment and biofilm. We explored these potential trade-offs in a novel experiment with replicated distal pipes to simultaneously evaluate the effects of water age, flush frequency, flow rate, pipe diameter, water heater temperature, disinfectant residual presence, and microbial regrowth in cold and hot pipes. In cold water, the total bacterial regrowth was controlled by WRT, plateauing after 3 days at cell counts 20 times higher than the influent water under a condition with little or no disinfectant. With a water heater operated at a warm setpoint of 40 °C, most regrowth occurred in the water heater tank, reducing the relative growth in the subsequent pipes. However, little regrowth occurred in the tank if operated at 60 °C with an influent chloramine residual, but cell counts increased 82 × above cold-water influent levels at 7.5 days WRT in the distal pipes. Legionella spp. and Mycobacterium spp. gene levels demonstrated divergent responses to flow rate. The highest levels of Legionella spp. (1.7 log higher than influent) were measured when flow velocity was >0.6 meters per second (mps), but the highest levels of Mycobacterium spp. gene copies (1.5 log higher than influent) were observed at the lowest flow velocity (0.1 mps) and highest water age. This study demonstrates the potential for differential impacts of water flow rate and WRT on regrowth in cold versus hot water pipes or for different OP pathogens.