In the mid 1700s the dockyard in Portsmouth was growing rapidly to counter the threat from the French, and the demand for flour to support both the naval and civil population increased dramatically. Sites for watermills besides the streams had all been developed so the entrepreneurs turned to tidal locations. Slipper Mill was amongst the 4 local mills built in this period. 

Slipper Mill and its tidal pond was built by Thomas Hendy in the 1760's as part of his development at the mouth of the River Ems.  Soil removed from the pond was used to enlarge Hendy's Quay along the west bank of the River Ems.  This is now occupied by the Kings Quay housing estate, but was formerly the site of a sawmill, boatyard and slipway, where JD Foster buil the famous Emsworth Oyster fishing fleet. The Echo, pride of the Emsworth Oyster smacks, was moored off Hendy's Quay until the 1950s.

By 1805 the pond had been extended north of Hermitage Bridge forming today's Peter Pond and by the mid-1880s the Mill was part of a complex of four working mills in Emsworth: Quay Mill at the bottom of South Street; the Old Flour Mill at the bottom of Queen Street; Lumley Mill; and New Slipper Mill (now Emsworth Marina).

The mill itself was built close to the bank over the water, with a large flanking store on the site of the present "Slipper Mill" building.  The mill was rebuilt on several occasions following fires caused by the very dusty atmosphere, with overheating bearings being the probable cause. 

In 1912 a great storm swept the mill house away and the miller and his family were relocated in the Roundhouse until Slipper Mill Cottage was built (by Quinnells (IoW) Ltd).

 
The mill was sold with a restrictive covenant in 1936, and finally ceased working in 1939 when electrical power from the National Grid was introduced.  Production and storage of animal feeds continued until the mid 1960s when the mill was demolished as was the former store which was converted into dwelling units for sale in 1970 (see newspaper article to the right).