Nanoflowers are a newly developed class of nanoparticles that show flower-like structures and attract much attention due to their simple preparation methods, high stability, and increased efficiency. The aim of the study is to investigate a strong alternative to reduce the severity of infection and increase the treatment of wastewater by exhibiting biofilm inhibition in medical and environmental applications of the ZnO-NFs with two different shapes. ZnO-NFs were synthesized by two different processes hydrothermal method (named ZnO–NF1) and the precipitation method (named ZnO–NF2). ZnO-NFs produced by two different synthesis methods were compared for the photocatalytic and antioxidant efficiency. The effects of Reactive Red 180 (RR180) and Basic Red 18 (BR18) dyes concentration, photocatalyst amount, and reaction time were investigated on dye removal efficiency for photocatalytic experiments. The color was completely removed for 25 mg/L BR18 and RR180 dyes for 75 min and 90 min, respectively, using 1.5 g/L photocatalyst amount using ZnO–NF1. However, 59.18% dye removal efficiency was obtained for 90 min by using a 1.5 g/L ZnO–NF2 photocatalyst for 25 mg/L BR18 dye removal, while a dye removal efficiency of 90.00% was detected for 90 min using 2 g/L ZnO–NF2 for 25 mg/L RR180 dye. Then, comparison of general properties such as antibacterial, antibiofilm, microbial cell viability, DNA fragmentation, antioxidant activities, and antimicrobial photodynamic therapy of ZnO-NFs were investigated. The antioxidant activity of ZnO–NF2 was found to be higher than ZnO–NF1 at each concentration (82.32% and 87.18% for ZnO–NF1 and ZnO–NF2, respectively, at 200 mg/mL).