In 2019, a tailings dam collapse in the Paraopeba River watershed (Minas Gerais, Brazil) released approximately 9.7 million cubic meters of iron ore tailings into the Ferro-Carvão stream, contaminating about 280 km of the Paraopeba River. This disaster deposited of tailings in the river channel and floodplain, severely altering aquatic ecosystems and biodiversity. In response, biomonitoring and recovery initiatives were launched under the Watercourse Recovery Program, part of the broader Degraded Area Recovery Program. These efforts focused on removing iron ore tailings via dredging and assessing its effects on aquatic assemblages. A sampling design was established with one upstream control site and five downstream sites in a 10 km reach, sampled biweekly starting in 2019—six months after the collapse and before dredging began. Biological indicators (benthic macroinvertebrates, zooplankton, phytoplankton, periphyton) were monitored alongside water quality, sediment, and habitat structure. Spatio-temporal analyses using alpha and beta diversity revealed that the most-affected assemblages were those closely associated with substrates (macroinvertebrates and periphyton). Spatial beta diversity showed that the most affected area lay between the first affected site and the penultimate site, characterized by turnover-driven instability and compositional changes. Nestedness explained beta diversity patterns between the control and first affected sites (i.e., the taxa of the first-affected site were a subset of the control site) and between the penultimate and last sites (i.e., the taxa of the last site were a subset of the penultimate site), delineating the boundaries of the greatest impact. These results occurred regardless of the position or activity of the dredge. Our findings indicate that ecological impacts were primarily linked to the dam collapse and seasonal factors, with localized dredging effects interacting with rainfall-driven disturbances. This study underscores the challenges of managing severely altered aquatic ecosystems and highlights the role of biomonitoring in guiding recovery efforts.