The territory of Lithuania is characterized by a prevailing moisture excess, therefore in order to timely remove excess water from arable lands, the drainage systems have long been installed. In order to drain excess water people used to dig trenches, to regulate (deepen or straighten) natural streams. The length of regulated streams has reached 46,000 km and they are deteriorated ecosystems. Investigations showed that the self-purification of streams from nitrates and phosphates is more effective in natural stretches than in stretches regulated for drainage purposes. Decrease in the average concentration of nitrates in natural and regulated stretches are 8.8 ± 5.0 and 3.0 ± 2.9 mg NO 3 − L−1, respectively. The average coefficient of nitrate self-purification, at a confidence level of 95% in natural stream stretches is 0.50 ± 0.22, and in regulated is −0.15 ± 0.21 km−1, and this difference is essential. The change in the average concentration of phosphates in natural and regulated stretches is almost the same, 0.2 ± 0.1 and 0.2 ± 0.2 mg PO 4 3 − L−1, respectively. The average coefficient of phosphate self-purification, at a confidence level of 95%, in natural stream stretches is 0.28 ± 0.12, in regulated −0.14 ± 0.12 km−1, and this difference is not essential. In terms of the need for the renovation of drainage systems it is suggested that soft naturalization measures are first applied in the streams of Western (Samogitian) Highlands, Coastal Lowlands, and South-Eastern Highlands to improve their self-purification processes.