Most studies of the impact of environmental factors on aquaculturally reared whiteleg shrimp Litopenaeus vannamei focus mainly on single factors, ignoring their combined effects. Thus, a four-factor three-level orthogonal experiment was designed to investigate the combined effects of ammonia nitrogen (NH3−N), nitrite (NO2−-N), salinity (S), and temperature (T) on L. vannamei over a 35-day period. Survival rate (SR), and daily growth in body length (DGL), and body weight (DGW) were lower at higher NH3-N and NO2−-N concentrations. DGL and DGW also increased at higher S, but increased at lower T and decreased at higher T. SR was most affected by NH3-N, whereas DGL and DGW were most affected by S. There was a significant interaction between NH3-N and T in all three growth indices, but none between NH3-N and S. Among the four serum physiological indices, NO2−-N had the greatest influence on blood urea nitrogen and ammonia, whereas the interaction of NH3-N and NO2−-N (INH3-N⁎NO2−-N) had the greatest effect on alanine aminotransferase and aspartate aminotransferase. NH3-N, INH3-N⁎NO2−-N, and INH3-N⁎S had significant effects on all four indices. Among the six hepatopancreatic physiological indices, NH3-N had the greatest effect on ATP content, Na+-K+-ATPase, and glutathione. Superoxide dismutase activity was most affected by NO2−-N, acid phosphatase activity by INH3-N⁎NO2−-N, and alkaline phosphatase activity by T. NH3-N had a significant effect, whereas INH3-N⁎NO2−-N had the most significant combined effect, on all six hepatopancreatic indices. At higher NH3-N and NO2−-N concentrations, numerous hepatocytes separated from the basement membrane, and the hepatic tubule lumen was mildly dilated, followed by hepatocyte degeneration and necrosis. These results provides a basis for the healthy aquaculture of L. vannamei.