The article deals with the auto-naturalization problems of regulated streams in Lithuania. Research on such streams overgrown with woody vegetation was conducted in the Neris River basin in the Baltic Highlands. We chose to investigate the most urbanized rough terrain area of southeastern Lithuania. The regulated streams found in this area include stretches with a relatively high reserve of hydraulic conductivity. Therefore, with reference to the Water Framework Directive for improving the ecological situation, we assessed the possibilities of promoting the naturalization process. The average density of woody vegetation on the investigated slopes of regulated streams is T = 1.26±0.20 items m-2. The slopes with northeastern exposure point to the average density of woody vegetation counting TNE = 0.91 items m-2, which is 2.42 times more than that observed on the slopes with eastern exposure and 2.30 times more than those with southern exposure (TS = 0.39 items m-2). Under the presence of the recent density of woody vegetation, hydraulic measurements established Manning’s roughness coefficient that varied from 0.030 to 0.094. The conducted simulation indicates that the studied stretches of regulated streams lose a margin of hydraulic conductivity when Manning’s roughness coefficient reaches a threshold of 0.060-0.080. Planning the naturalization of regulated streams is first offered in the stretches of higher slopes (S0>0.003), where the maintenance of the adequate roughness of the bed may assist in designing the overgrowth of both slopes with woody vegetation.