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Careful management and monitoring of irrigation systems are very important for sustainable use of water resources and efficient use of water by crops. Also, new developments in filtering technologies are necessary to reuse eutrophic water in irrigated fields. In order to prevent biological and chemical clogging in a microirrigation system, monitoring experiments of filters and emitters have been conducted since 1990 in the Tohaku National Irrigation Project (TNIP), Japan. The fields have fertile Kuroboku (volcanic ash) soils and intensive livestock industry within the river basin of the TNIP. These conditions promoted water pollution and growth of planktons, shells and other organisms in the farm pond and/or reservoir. The clogging of filter elements of the auto-screen filtration system occurred with metals rusted by Mn and Fe ions in the irrigation water. The metal rust was effectively removed by preserving in cleaning materials for a few days every half year, after taking out the element from the filtration system. Micro showering emitter lines applied to soybean and lawn fields also had nozzle clogging due to shells, which were effectively removed by disc and/or screen type secondary filters. Plant and animal planktons clogged at the emitter of the mist spraying tube of watermelon fields grown in plastic greenhouses. Regular cleaning inside the mist spraying tube with flexible porous materials during irrigation effectively prevented this clogging.