Irrigation canals and open drains can be contaminated by domestic, industrial and agriculture waste. Weed earth or aquatic macrophytes (emergent, floating, leaved, Submerged and algae) infection can seriously impeded the flow of canal water not only in tropical conditions but also in semi-arid climates. Another hazard of weed infection is the shelter and good breeding conditions. They offer for vectors (mosquitoes, snails etc.) of debilitating diseases. The lake of interest by farmers in participating in maintenance work is the main reason for state of disrepair of the tertiary canals as water courses for which the farmers may have been made responsible. The aim of this study is to protect the environment from diseases by reducing floating plants and weeds growth as well as increase of cross sections area of both irrigation and drain canals therefore, reduce leakage of available water and improve the equity of water distribution. For conducting two sites have been selected; Therefore, the first site is Ezbet El-Nusra at Kafer El-Sheikh, and the second is Ezbet El Qasr at El-Behira governorate. Water sample are collected from the selected canals and drains at three check points (first, middle and end) at three times (before and after cleaning). Sediments, floating plant and weed samples are taken from the same check point. Discharge and cross sectional measurements take place in the work. The results showed that: macro, micronutrients and heavy metals before and after cleaning are considerably below the permissible limits in all investigated sites. Ammonium-N concentration at the upstream of the irrigation canals is exceeded the critical limits for irrigation which indicated that an anaerobic condition taking place. Total and fecal coliforms values of both canals and drains of the collected water samples show a clearly decrease after cleaning process in Kafer El-Sheigh investigated area. Salmonella & Shigella are found in high values of canals and drains and followed the same trend of total and feacal coliforms. The Chemical and biological oxygen demand of irrigation canals and drains show high level of COD & BOD exceeding the maximum limits and decree of agriculture reuse (unrestricted crop) in Egypt. Except of the first location of drainage canal which is below the permissible limit. All the collected water samples of both irrigation and drain canal of Kafer El Sheigh and El Beheira are contaminated with Entamiba coli and plantidium coli before and after cleaning ditches the determined chlorophyll (A & B) of the collected water samples from irrigation and drain canal of Kafer El Sheigh and El Beheira are in excellent category due to its less than they permissible limit (<3 mg l^-1) before and after cleaning the ditches.