Waterlogging and its associated soil salinity are a major impediment to the sustainability of irrigated agriculture. Although conventional engineering drainage technologies such as subsurface or vertical drainage combat the problem, they are costly and generate huge quantities of effluent which is difficult to dispose of. Biodrainage, which removes excess soil water by deep‐rooted fast‐growing trees through evapotranspiration using bioenergy, is an appropriate alternative. Plant consumptive water use varies between 6500 and 28 000 m3 ha‐1 yr‐1 and an ideal tree plantation lowers groundwater tables by 1–2 m over a time period of 3–5 years. Trees such as Eucalyptus, Populus, Casuarina, Dalbergia, Syzigium, Acacia, Prosopis, Leucaena, etc. are found to be effective in lowering shallow groundwater tables and reversing salinity trends. Integration of trees such as Eucalyptus and Populus along with crops in a unified agroforestry system, on approach roads, field bunds or on dykes of ponds in an integrated farming system, is another viable proposition. Irrigation of highly transpiring trees has also been proposed for reuse of wastewater and conservation of nutrient energy into biomass, leading to carbon sequestration, environmental sanitation and eco‐restoration. For effective understanding and implementation, several case studies on the role of biodrainage for managing waterlogging and salinity are discussed in this paper. Copyright © 2018 John Wiley & Sons, Ltd.