Shower systems create conditions conducive to the growth of opportunistic pathogens, but the timing and location of associated risks are poorly understood. In this study, we constructed 48 full size shower units with six incubation periods (4, 10, 16, 22, 30, and 40 weeks) and four water heater temperature (39, 45, 51, and 58 °C) to examine the dynamics of microbial growth and pathogen distribution. Results showed that during the initial stage (4 weeks), peak biomass was observed for all biofilms, ranked as shower hose (SHE) > cold-water pipe (CWP) > hot-water pipe (HWP), followed by a sharp decline by the 10th-week. At the 4th-week, the biofilm was loose and easily detached into the water, possibly promoted by leached organic carbon from plastic material, fostering the growth of specific microorganisms. The impacts of stagnation and temperature became more pronounced in CWP and HWP over time. Legionella pneumophila appeared in biofilms at the 4th-week, disappeared, and reappeared in large numbers since the 22nd-week. Differently, Mycobacterium spp. emerged in large numbers after 30 weeks. Both pathogens were notably enriched in showerheads and shower hoses. This study highlights critical periods of higher risk in shower systems, particularly in the early stages (4 weeks) and after 22 weeks, suggesting that risks can be mitigated by pre-soaking pipes or regularly cleaning (e.g., heat shock flushing) and replacing showerheads and hoses.