To evaluate the aquatic hazards of the insect juvenile hormone analogue fenoxycarb, a single application (0, 48.8, 156.3, 500, 1600, and 5120 μg/L) of it was done in indoor freshwater systems dominated by Daphnia carinata (daphnid) and Dolerocypris sinensis (ostracoda). The responses of zooplankton (counted by abundance and the activity and immuno-reactive content of free N-Acetyl-β-D-glucosaminidase (NAGase)), phytoplankton (counted by chlorophyll and phycocyanin), planktonic bacteria and fungi, and some water quality parameters were investigated in a period of 35 d. Results of the study showed that the ostracoda was more sensitive than daphnid, with time-weighted average (TWA)-based no observed effect concentrations (NOECs) to be 8.45 and 12.66 μg/L in systems without humic acid addition (HA−) and to be 6.37 and 9.54 μg/L in systems with humic acid addition (HA+). The duration of treatment-related effects in the ostracoda population was longer than the daphnid population (21 vs. 14 days). Besides, the data analysis indicated that the toxicity of fenoxycarb was significantly enhanced in the HA+ systems. Owing to the reduced grazing pressure, the concentrations of chlorophyll and phycocyanin increased in the two highest treatments. The increase in photosynthesis along with a reduced animal excretion led to an increase in pH and a decrease in nutrient contents. These changes seemed to have an effect on the microbial communities. For example, the abundances of some opportunistic pathogens of aquatic animals (e.g. Aeromonas and Cladosporium) and organic-pollutant-degrading microorganisms (e.g. Ancylobacter and Azospirillum) increased significantly in microbial communities, but the abundances of Pedobacter, Candidatus Planktoluna, and Rhodobacter (photosynthetic bacteria) markedly decreased. This study provides useful information to understand the ecotoxicological impacts of fenoxycarb at the population and community levels while integrating the effects of HA on toxicity.