Although many wetlands have been lost, the European lowlands still hold a mosaic of aquatic habitats covering rivers, lakes, ponds, ditches, springs, and swamps. To effectively conserve this diverse and important resource, both scientific studies and management and restoration activities need to focus on all of the watery patches in the landscape and in turn on the linkages between them. Over recent years, catchment and landscape‐based approaches to aquatic conservation have been on the rise. However, perhaps driven by a lack of legislative drivers, there remains a tendency to neglect small lakes, ponds, and headwater streams. With consideration of the current conservation scene in the UK, and using a small lowland river catchment (River Glaven, eastern England) as a case study, this paper outlines the strong need for an integrated approach to aquatic conservation that sees rivers, lakes, and ponds as habitat networks. It is proposed that river restoration needs to more fully embrace standing water habitats on floodplains (backwaters and ponds), frequently missing components in regulated rivers. Equally, is it argued that aquatic conservation strategies should focus more strongly on headwater areas where protecting/restoring networks of farmland ponds, ditches, and small streams should increase connectivity for aquatic species, while moderating floods and improving water quality for receiving systems. In this way, aquatic conservation should become a much more effective and sustainable activity with positive ecological consequences that cascade downstream and into the coastal zone. WIREs Water 2014, 1:573–585. doi: 10.1002/wat2.1045This article is categorized under: Water and Life > Conservation, Management, and Awareness Water and Life > Stresses and Pressures on Ecosystems Science of Water > Water and Environmental Change