This study aimed to understand the characteristics of zooplankton community structure and their association with environmental factors in different sources of drinking water. A seasonal investigation was conducted on zooplankton from two drinking water sources (8 rivers and 8 reservoirs) in Zhejiang Province, China, from January 2010 to October 2011. A total of 21 dominant species (genus) of zooplankton (8 Rotifera, 5 Cladocera, 5 Cyclopoida, and 3 Calanoida) were recorded. The primary dominant species in each group of zooplankton were Polyarthra trigla, Bosmina longirostris, Thermocyclops dybowskii, and Sinocalanus dorrii, respectively. Nine of the dominant species (genera) were at the same time indicator species of water trophic state. The more frequently that indicator species of trophic state occurred, the more comprehensive the trophic level index (TLIc) (P < 0.01) of the rivers was. Over the 2-year study period, the average density of zooplankton in the rivers and reservoirs was 345.2 L^-1 and 199.4 L^-1, respectively, while the biomass was 0.667 mg/L and 0.421 mg/L, respectively. Rotifer and copepod nauplii dominated both the rivers and reservoirs, representing 87.9% and 88.3% density, respectively. Crustaceans were mainly Cyclopoida, which had 2 times the biomass of Calanoida in the rivers, whereas Calanoida had 2 times the biomass of Cyclopoida in the reservoirs. The river community density (biomass) coefficient of variation ranged between 158.2% and 325.5%, while that of reservoirs ranged between 107.8% and 345.2%. The results of the stepwise regression analysis showed that the correlative coefficient between the density (biomass) of the zooplankton community and the water quality factors was much higher in the rivers (P < 0.01) than in the reservoirs (P < 0.05). Total phosphorus (TP) and ammonia nitrogen primarily occurred in the rivers and the reservoirs in all effective regression equations, respectively. Path and decision coefficient analysis showed that TP and chlorophyll a (Chl.a) content in the rivers had a positive effect on the population dynamics of the zooplankton community (rotifers, copepod nauplii, and Cyclops), whereas dissolved oxygen content had a negative effect. TP was the most important factor affecting population dynamics of rotifers, copepod nauplii, and Cyclops in the rivers, whereas Chl.a was the most important factor limiting the communities growth. The reservoir fishery resources aquaculture might cause zooplankton abundance to decline, the Calanoida community to gradually disappear, and the water trophic state to transform from nitrogen limitation conditions to phosphorus limitation conditions. The river community (rotifers, copepod nauplii, and Cyclops) density (biomass) had a significant linear regression relationship with the water trophic index TLIc_Density (TLIc_Biomass) (P < 0.001). Copepod nauplii density constituted a limiting factor for TLIc_Density, due to its maximum average coefficient of variation (261.8%). Rotifer biomass constituted a limiting factor for TLIc_Biomass, due to its maximum average coefficient of variation (257.9%). The average variation coefficient of Cyclops density (biomass) was moderate, with small fluctuations; thus, this group represented the most important and stable water quality indicator. The study results provide an important reference for selecting specific expansion indicators of the zooplankton community in water quality monitoring. None of the zooplankton community density (biomass) groups in the reservoirs had any significant linear regression relationships with the water TLIc (P > 0.05).