Until 1999, the village comprised three parishes, Saltfleetby St Peter, Saltfleetby All Saints and Saltfleetby St Clement, each one centred on the church that gave it its name. However, the village has operated as one entity for many years. The hamlet of Three Bridges is south of Saltfleetby St Peter.
A section of the village seashore is part of the Saltfleetby-Theddlethorpe Dunes National Nature Reserve, which has sea dunes and both saltwater and freshwater marshes. The reserve is one of only five places in the UK where the natterjack toad is found.