Sustaining environmental flows (e‐flows) is a basic requirement for river, lake and marsh management. Rivers, lakes and marshes have close hydrological and ecological connections in a river basin, and form river–lake‐marsh systems. Any measure that is designed to address problems related to only one of these water bodies in isolation of the others may lead to unexpected, undesired and sub‐optimal consequences for one or all of the water bodies. Papers were selected for this special issue ‘Environmental Flow Mechanism and Management for River‐Lake‐Marsh Systems’ to illustrate recent advances in revealing new mechanisms connecting hydrological and environmental/ecological processes, developing new methods for e‐flow calculation, and establishing new measures for e‐flow management.