Technically the Crown 'owns' the sea - certainly between the high water mark and the 3 mile limit. Hence the Crown commisioners make a considerable sum from moorings, fish farms, outfalls - you name it.
More relevently they are a considerable number of bodies which have authority over the harbours, estuaries and oteher selected areas. They are the ones who generally have prohibited the operation of seaplanes within their areas of authority either by direct ruling or blanket maximum speed limits - as per the Lake District and Norfolk Broads.
If you want permission to operate they you use your 'considerable' research skills to get hold of the local byelaws covering the area you are looking at. If not specifically prohibited you then need to apply for permission. It will almost inevitably have to be in writing - because these are all quango council type bodies - and inevitably they will take some time - need to include it at the next committee meeting. There is a prob 90 that it will be declined on 'elfin safety grounds by people who have no knowledge or understanding of seaplane operations.
But if you get permission there is only the corrosion to worry about!!! (Oh and somewhere to moor, and get fuel, and not get damaged (or sink).