Constructed flood mitigation and drainage systems are integral to the development of many estuarine floodplains. These systems function throughout the tidal range, protecting from high water levels while draining excess catchment flows to the low water level. However, drainage can only be achieved under gravity when suitable water levels are available for discharge. Changes to the tidal range and symmetry that occur throughout estuarine waters mean that the window of opportunity for gravity discharge will vary dynamically within and between different catchments. It will also be affected by sea level rise (SLR). Concerns regarding the impacts of SLR have focussed on the acute effects of higher water levels, but SLR will affect the full tidal range and drainage systems will be particularly vulnerable to changes in the low tide. This study introduces the concept of the “drainage window”; to assess how the tidal regime may influence the drainage of estuarine floodplains, and particularly the potential impact of changing tidal regimes under SLR. The results of applying the drainage window to two different estuaries indicate that SLR may substantially reduce the opportunity for discharging many estuarine floodplain drainage systems. Additionally, measures proposed to mitigate flood risks may exacerbate drainage risks. Reduced drainage creates a host of chronic problems that may necessitate changes to existing land uses. A holistic assessment of future changes to all water levels (including low tide water levels) is required to inform strategic land use planning and management.