The authority of Trinity House was frustrated when the Brethren wanted to put forward an official register of all seamarks and there were many objections. In 1566, Trinity House was recognised as the Custodian of all British Seamarks, but the owners of the Cinque Ports strongly objected on the grounds that their own income would be seriously eroded. Numerous landowners also petitioned Queen Elizabeth, because the Act encompassed church spires, tall trees and houses as navigational aids. More importantly, it gave Trinity House the power to impose fines if any of these land-based seamarks were removed without the Elders' permission [Pepys, ,VII].
To add to the confusion, all ship masters closely guarded their sea charts and 'Rutters' (books of sailing directions) which made it necessary for Trinity House to prove the masters actually used these land-based marks for navigation before a levy could be imposed. As the Act said that Trinity House must be self-financing, suitable lights could not be built without the proper funds. Trinity House continued to petition the Privy Council but, as usual, the power of the Lord High Admiral was upheld for it was he who gained from the levies.
As the Corporation's influence grew, its achievements were finally rewarded when, on the 13th January 1573, Trinity House was granted its Coat-of-Arms with the motto, "Trinitas in Unitate." The Brethren were led to believe that the office of the Lord High Admiral would be forced to surrender the rights to collect the shipping levies in favour of the Corporation. Instead the Coat-of-Arms was all that was issued, formally granted by Elizabeth I and presented by Sir Gilbert Dethicke, recorded on the documents as the 'Knight of the Garter, Principal King of Arms and Chief Officer of Arms for the most honourable Order of the Garter'.
On the 11th June 1594 a new Charter was issued to Trinity House by William Brench, on behalf of Queen Elizabeth I.
"And whereas he [Admiral Howard] hath...surrendered...all his right... in... erecting...any beacons, buoys, marks and signs for the sea...it is in and by Our Statute or Act of Parliament made in the eighth year of Our reign, specially and expressly ordained and enacted, that the said Master, Wardens and Assistants of the Trinity House of Deptford-Strond...might lawfully...at their costs and charges, make, erect and set up, such and so many beacons, marks and signs for the sea, in such...places...as to them shall seem most meet, needful and requisite, whereby dangers may be avoided and escaped, and ships the better come to their ports without peril".
Trinity House was now fully recognised as superintendent of all seamarks and the only authority for collection of dues for beaconage and ballastage. The Act commanded that if these were destroyed or removed the beacons, marks and signs for the sea must be erected instead. Notably, lights were not specifically mentioned. This statute further enacted that none of the accidental seamarks should be removed or cut down upon a penalty of a hundred pounds, and if the owner was not worth that sum, he should be convicted of outlawry.
The other important issue dealt with in the Charter was ballastage which had been the source of great argument and envy. Ballastage was officially "gravel, sand and soil of the Thames" which the operator was to "land and lay on shore upon any of our waste ground"; it was forbidden to "sell, vend, give or utter any gravel, sand or soil without the licence" of the ballast owner or owners.
Dealings in ballast were two-fold, firstly, the dredging up of sand and shingle from the river bed to keep the channels and wharfages clear, and secondly the supplying of gravel to ships to serve the purpose of steadying them when light and unladen. All vessels in the Thames, His Majesty's as well as others, obtained their shingle and gravel from the ballast owners. Therefore the only way it could be done on a profitable basis was to make it a monopoly and compel the ship Master to get his gravel from accredited ballast mongers.
The monopoly of ballastage, one of the first monopolies of all, was a privilege of Lord High Admirals of England who could sub-let the rights to others. It first went to the Earl of Surrey who in 1517 sub-let the ballasting of ships to Thomas Spert who paid a rental of £10. In 1541 there were further sub-rentals by the Earl of Russell to various persons in respect of Rotherhithe and Limehouse, and so forth by different Lord High Admirals to other people.
On the 8th July 1578, the position of Lord High Admiral was conferred on Lord Charles Howard, Baron of Effingham. It seemed that one of his first duties would be to address the problem of the beaconage and ballastage levies, for the Privy Purse was running low, but pressure from the Privy Council stopped investigation. Under pressure, Howard indicated to Her Majesty Queen Elizabeth that she could have the ballastage rights. Part of the 1594 Charter read,
"Whereas...Charles, Lord Howard...baron of Effingham, and our great Admiral of England, hath...absolutely surrendered...the lastage and ballastage...of all...ships...in or upon the river of the Thames, betwixt Our city of London and the main sea...and all his lawful right...which he hath...by virtue of the said office of Great Admiral of England..We will be pleased to give, grant and confirm the premises unto the Master, Wardens and Assistants of the Trinity House of Deptford-Strond, in Our county of Kent.
Obviously,the monarch would not administer the ballastage personally so it was decided that Trinity House was the best and most deserving organisation to be given it.