Active flow control using automated gates and weirs aims to utilise available dispersed storage within sewer systems to alleviate the severity and frequency of localised flooding incidents. Whilst a previous study has demonstrated its potential, a key operational concern before implementation was sedimentation. An experimental programme was designed to investigate the sediment deposition created when using a flow control device. Tests were also undertaken to examine the potential for rapid gate opening to flush away any resulting deposits. In catchments dominated by fine material in suspension, the use of an active flow control device can result in a uniformly thick deposit upstream of the gate. Rapid gate opening results in deposited material eroding in large sections starting at the gate and moving in an upstream direction. Granular sediment forms a series of discrete bedforms which are fairly uniform regardless of the flow conditions and a larger deposit further upstream. The potential for flushing granular deposits is limited and modification of the operation of the gate has shown little potential for increasing the effectiveness. Therefore, active flow control using a single downstream gate may only be suitable in systems with fine material moving in suspension during dry weather flow and not where there is significant granular sediment.