Since November of 2015, when ore tailings from a dam rupture reached the Atlantic Ocean, researchers are trying to assess the degree of impact across the Doce River and adjacent coastal area. This study aims to use the zooplankton dynamics as a tool to evaluate the environmental impact in the coastal region, five years after the rupture, during periods of low and high river flow. Doce River flow varied from 49 to 5179 m ³/s and structured the zooplankton community between periods of low and high river flow, but salinity and chlorophyll-a had stronger correlation with depth (r = 0.40 and − 0.40 respectively) than with the Doce River discharge variation along the sampling period (r < 0.2). On the other hand, inorganic particles in the water and total metal concentration (dissolved + particulate), used as tracers of the iron enriched tailing (Al, Cd, Cr, Cu, Fe, V), were correlated with fluvial discharge and showed to be the main factor driving the zooplankton community dynamics. For assessing the degree of environmental impact, we tested the ecological indexes for the zooplankton community. Margalef Richness, Pielou Evenness and Shannon-Wiener Diversity varied from 2.52, 0.40 and 1.39 (all registered during high river flow period) to 9.02, 0.85 and 3.44 (all registered during low river flow period), respectively. Along with those community indicators, we evaluated the response of representative taxonomical genera such as Paracalanus, Oikopleura and Temora, regarding the Doce River flow, and found population patterns that established a baseline for future monitoring in the region. Our results showed that the zooplankton community is more fragile when the river discharge is stronger, and this pattern is confirmed by all indicators tested.