Social development and environmental pollution have worsened the scarcity of global water resources. Recycling filter backwash water (FBW) can enhance water resource efficiency. Systematically investigating the biological risk of FBW for public health is essential. Biological risks such as widely publicized pathogens, emerging antibiotic resistance genes (ARGs), and virulence factor genes (VFGs) were studied. The sand filter backwash water (SFBW) and biological activated carbon filter backwash water (BACFBW) from a DWTP in southern China were sampled over two years. Pathogens and community structure were investigated using 16S and 18S rRNA gene sequencing. ARGs and VFGs were studied using metagenomic sequencing. The BACFBW contained 110 pathogens, 37 ARGs, and 740 virulence factors (VFs), and the SFBW contained 103 pathogens, 75 ARGs, and 832 VFs. The relative abundance of pathogens was higher in summer than in winter for BACFBW. The richness of both ARGs and VFGs in SFBW was higher than in BACFBW. Shortening the backwash cycle could reduce the relative abundance of pathogens in FBW but had no significant effect on ARGs and VFGs in FBW. BACFBW in summer can be reused after appropriately shortening the backwash cycle when controlling the risk of pathogens. The risk of SFBW cannot be reduced by shortening the backwash cycle when controlling ARGs and VFGs. This study provided a basis for safely reusing the sand filter backwash water and biological activated carbon filter backwash water.