Approaches
Entering the Piscataqua is not especially challenging. The mouth of the river is wide and deep, with only a few well-marked ledges on the starboard side. Currents at first are significant but not overpowering -- running at a knot and a half or so in the stretch of river below Fort Point. As the river turns west and narrows above Fort Point, however, the currents get stronger, approaching three knots in the vicinity of Seavey Island.
Anchorages
The only anchorage for small boats in Kittery -- and it's a pretty good one -- is in the western side of Pepperrell Cove, underneath Fort McClary. There is room here for maybe a dozen boats to anchor outside the mooring area and clear of the river in depths ranging from 10 to 20 feet at low. The anchorage is far enough out of the channel that currents are minimal.
Protection is good from southeast up to north and around to west; to the southwest the anchorage is exposed to the moderate fetch across the river. The Cove is essentially wide open to the south, however, down about two miles of river to the ocean. When low pressure approaches from the west Pepperrell Cove mostly becomes a lee shore.
Moorings
The moorings in Pepperrell Cove are slightly more sheltered than the anchorage, as they are further in behind Fishing Island and the surrounding ledges. But they are still exposed to weather from the south.
The Portsmouth Yacht Club has six guest moorings (which may be reserved) in the Cove. The club launch serves their moorings here. As recently as 2010, some of these mooring balls were still labelled "PCYC" from the now-defunct Pepperrell Cove Yacht Club.
The Kittery Harbormaster may have a mooring available, but most of his are for resident boats. There is a plan for a string of town-controlled visitor moorings in the future.
The other source for moorings on the north side of the river is the Kittery Point Yacht Yard, the long-time Dion's yard under current management since 2004. Their mooring field and shoreside facilities in the Back Channel behind Seavey Island are in the harbor's most protected water downriver of the bridges. Not much weather can get in here, but the current does flow through with more than expected strength. Mooring landings that don't take into account the force of the current here can get exciting in a hurry.
Note that the little cove between Clarks and Seavey Islands is a restricted area for the Portsmouth Naval Ship Yard. Boats may not enter the cove without Yard permission.
Slips
There are no slips in Pepperrell Cove. For short-term business you can land at the town dock, with better than 10 feet at low. There is a channel of small uncharted buoys leading the way in.
KPYY's slips are primarily for their service business, but it's possible that dock space is available for visitors.
Portsmouth
On the Portsmouth side of the river, there are guest moorings at the Portsmouth Yacht Club and dock space for visiting boats at the city-owned Prescott Park, just downstream of the first bridge.