Macroalgal blooms can trigger adverse biogeochemical conditions at the sediment-water interface of shallow coastal areas, hence threatening critical habitats such as seagrasses meadows. The direction and magnitude of macroalgal blooms impacts on the aquatic ecosystem can be context-dependent, varying according to the local hydrodynamic conditions. Thus, studies investigating the impacts of stagnant algal depositions on the benthos may fail to address realistic situations and interactions which are common in well-flushed systems. This is especially true for the South America coast, where no study has investigated the effects of macroalgal blooms on seagrasses meadows. To fully understand the impacts of macroalgal blooms on sediment biogeochemistry and seagrass habitats across distinct environmental conditions and biogeographical regions, two independent, complementary field experiments replicated the natural temporal patterns of drift macroalgal mats depositions on unvegetated and vegetated (Ruppia maritima meadows) shoals of the Patos Lagoon estuary (PLE), a subtropical, high hydrodynamic system in southern Brazil. Transitory depositions of algal mats alleviated deleterious biogeochemical conditions in the sediment-water interface of unvegetated bottoms. Nevertheless, these unstable algal depositions promoted significant reductions in R. maritima biomass, by reducing their shoot height and density, and rhizome length. That plant biomass reductions were followed by a decrease in the abundance of the dominant infaunal tanaidacean Monokalliapseudes schubarti, indicating that algal impacts on seagrasses were transferred to higher trophic levels. Our results suggest that, although unstable deposition of drift algal mats can attenuate potential adverse impacts at the sediment-water interface, the physical stress during mats advection can still trigger small seagrass losses. This process may diminish the resilience of R. maritima meadows in the PLE, with impacts on estuarine nutrient cycling and secondary production. We conclude that, although harmful drift macroalgal blooms area global phenomenon, the mechanisms through which macroalgae impair seagrass habitats may vary according to the environmental context. Therefore, further studies are necessary to identify the underlying mechanisms of drift macroalgae-seagrass-macrofauna interactions in high hydrodynamic systems and their generality across distinct biogeographical areas.