The discharge of antibiotics and metals in estuaries is of great concern since they threaten microbial communities that are critical for maintaining ecosystem function. To understand single and combined effects of norfloxacin (0–20 μg g−1) and copper (40 μg g−1) on microbial ecology in estuaries, we evaluated changes in bacteria population, inhibition rates, and microbial composition in estuarine sediments over a 28-day period. Bacteria population significantly decreased following single and combined exposure to norfloxacin and copper throughout the incubation period, except on Day 28 in treatments exposed to copper, 20 μg g−1 norfloxacin, or both. These three treatment groups had lower Shannon diversity and Simpson's indices on Day 28 than other treatments and the controls suggesting recovery in bacteria population did not correspond with recovery in richness and evenness. Furthermore, functional predictions revealed that the effect of time and contaminants were significantly different on some microbial community functions on Day 28, especially the combination of Cu and high concentration NFX, including aerobic chemoheterotrophy, methanol oxidation and methylotrophy. Thus, norfloxacin and copper had significant adverse effects on microbial communities in estuarine sediments; however, the combined effects were variable and depended on exposure duration and antibiotic concentration.