Viral diseases are major emerging problems of shrimp that have affected the production, and even complete losses for shrimp farms. In this study, we developed a sensitive TaqMan real-time PCR method to quantify white spot syndrome virus (WSSV) and hepatopancreatic parvovirus (HPV) in the shrimp and pond water in which fleshy shrimp, Fenneropenaeus chinensis, and Pacific white shrimp, Litopenaeus vannamei, are reared. WSSV and HPV in pond seawaters ranged from $1.65{ imes}10^3$ to $2.43{ imes}10^9$ and from 0 to $4.43{ imes}10^5$ copies/L of seawater, respectively. Of 20 ponds analyzed, all pond water and shrimp were positive for WSSv. L. vannamei showed higher susceptibility to WSSV than F chinensis. HPV was detected only in the pond water for F chinensis. In shrimp tissue, however, HPV was found in both species, with 23-times higher infection rate in F chinensis than L. vannamei. The total bacterial counts in the pond water ranged from $2.23{ imes}l0^3$ to $1.98{ imes}l0^5;CFU/mL$. The variations in total bacterial count for each pond appeared to correlate to the variations of the WSSV load. Statistical analysis indicated that there was no significant difference (P>0.05) between the WSSV load in pond water and shrimp, and there was no relationship between total bacterial load and viral load in the pond water. However, a significant difference (P<0.01) was found between HPV load and L. vannamei and F chinensis pond water.