Ecological risk assessment of chemicals in mesocosms requires measurement of a large number of parameters at the community level. Studies on invertebrate communities usually focus on taxonomic approaches, which only provide insights into taxonomic structure changes induced by chemicals. In the present study, abundance, biomass (B), theoretical production (P), and instantaneous P/B ratio were used as endpoints to assess the effects of the commercial form of the dithiocarbamate fungicide thiram (35 µg/L and 170 µg/L nominal concentrations) and of the hydrocarbon water accommodated fraction (HWAF) of a petroleum distillate (0.01 mg/L, 0.4 mg/L, 2 mg/L, and 20 mg/L loadings) on the zooplankton community in freshwater pond mesocosms. Endpoints were measured during a 4-wk treatment period (1 pulse/wk) followed by a 5-mo posttreatment period to evaluate zooplankton population recovery. The chlorophyll a concentration in water was significantly increased after treatment with HWAF, whereas it was not affected by thiram treatment. Zooplankton abundance-based analysis showed effects on a limited number of taxa, whereas other endpoints (mainly the P/B ratio) revealed that more taxa were impacted, with recovery depending on the chemical and concentration. Exposure to HWAF mainly had a negative impact on cladocerans, which resulted in top-down effects (between cladocerans and phytoplankton). Thiram negatively affected rotifers and copepods, suggesting more direct toxic effects. The results show that the use of secondary production as an endpoint provides a more comprehensive assessment of potential direct and indirect effects of chemicals on a community, and they also support evidence of alteration in functional processes.