Nanofiltration membranes are highly effective in removing low -molecular weight compounds, which include the secondary metabolites 2-methylisoborneol (2-MIB) and 1,10-dimethyl trans-9-decalol (Geosmin), produced by cyanobacteria and difficult to remove by conventional treatment processes. Considering that high retention and permeate flux are important characteristics in the process, this study aimed to evaluate the efficiency of the NF90 membrane pretreated with water and 50% (v/v) ethanol solution in the retention of 2-MIB and Geosmin, considering the application of low constant working pressure values of 4, 7, and 10 bar and evaluating its permeability to water and metabolite retention capacity. Retention was evaluated from a concentration of 100 ng L-1 of 2-MIB and Geosmin for 120 min of filtration time. The occurrence of fouling was also evaluated, noting that there was no fouling. At the three pressure values considered, membranes pretreated in 50% (v/v) ethanol solution showed a higher permeate flux (91.4 Lm-2 h-1 at 225.4 L m-2 h-1) than that observed for membranes treated in water (34.08 L m-2 h-1 at 59.14 L m-2 h-1). As for retention, no significant differences were observed between the membranes, with removals of 93 and 99% being obtained for membranes pretreated in 50% (v/v) ethanol solution and water, respectively. It can be observed that the pretreatment conserved the efficiency in the retention of compounds and provided an improvement in the physical and chemical characteristics of the membrane, allowing the achievement of permeate fluxes greater than those observed with the membrane pretreated in water.