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Eutrophication has led to the widespread occurrence of cyanobacterial blooms. Toxic cyanobacterial blooms with high concentrations of microcystins (MCs) have been identified in the Lalla Takerkoust reservoir in Morocco. The objective of this study was to evaluate the efficiency of the Multi-Soil-Layering (MSL) ecotechnology in removing natural cyanobacterial blooms from the lake. Two MSL pilots were used in rectangular glass tanks (60 × 10 × 70 cm). They consisted of permeable layers (PLs) made of pozzolan and a soil mixture layer (SML) containing local soil, ferrous metal, charcoal and sawdust. The main difference between the two systems was the type of local soil used: sandy soil for MSL1 and clayey soil for MSL2. Both MSL pilots effectively reduced cyanobacterial cell concentrations in the treated water to very low levels (0.09 and 0.001 cells/mL). MSL1 showed a gradual improvement in MC removal from 52 % to 99 %, while MSL2 started higher at 90 % but dropped to 54% before reaching 86%. Both MSL systems significantly reduced organic matter levels (97.2 % for MSL1 and 95.8 % for MSL2). Both MSLs were shown to be effective in removing cyanobacteria, MCs, and organic matter with comparable performance. [Display omitted] • Cyanobacterial cell removal by Multi-Soil-Layering (MSL) ranged from 99 % to 100 % • Greater degradation capacity of MC-LR in MSL1 (sandy soil) and MSL2 (clay soil) • MC-YR variant was most persistent in substrate of both MSL systems • qPCR detected degrading bacteria in both MSL systems • MSL1 had significant abundance of mlrA gene copies and degrading bacteria [ABSTRACT FROM AUTHOR]