In a previous post, we read Halley’s letter to the Lords of the Admiralty proposing a new voyage to make “an exact account of the Course of the Tides on and about the Coast of England”, which he claimed would be “a work of generall Use to all Shipping”. Their lordships quickly approved his proposal, and Halley set sail on his third voyage on 14 June 1701 – but what exactly was he doing? Here’re the Admiralty’s instructions:
Whereas his Maj[es]ties Pink the Paramour, is particularly fitted out and Putt under your Command that you may proceed with her, and observe the Course of the Tydes in the Channell of England, and other things remarkable, You are therefore hereby required and directed to proceed with the Said Vessell, and use your utmost care and Diligence in observing the Course of the Tydes accordingly, as well in the Midsea as on both shores; As alsoe the Precise times of High and Low Water of the Sett and Strength of the Flood and Ebb, and how many feet it flows, in as many, and at such certaine places, as may Suffice to describe the whole. And whereas in many places in the Channell there are Irregular and halfe Tydes you are in a particular Manner to be very carefull in observing them.
And you are alsoe to take the true bearings of the Princip[a]l head Lands on the English Coast one from another, and to continue the Meridian as often as conveniently you can from side to side of the Channell, in ord[e]r to lay downe both Coast truly against one another.
And in case dureing your being employed on this Service, any other Matters may Occur unto you, the observing and Publishing whereof may tend towards the Security of the Navigation of the Subjects of his Maj[es]tie or other Princes tradeing into the Channell you are to be very carefull in the takeing notice thereof: And when you Shall have p[er]formed what Service you can, with relation to the particulars before menc[i]o[n]ed, you are to returne with the Ship you Command into the River of Thames, giving Us from time to time an Account of your Proceedings Dated this 12° June 1701 
These instructions can be summarised as:
- to make observations of the behaviour of the tides in the Channel and along the English and French coasts
- to take bearings that will allow the French and English coasts to be correctly situated north-south from one another
- to take note of anything else that might lead to safer navigation in the Channel for traders
The first two points were copied almost verbatim from a letter of Halley’s dated the previous day (11 June), but the third point was added by the Admiralty, and it’s been suggested that it might represent an order for Halley to gather intelligence from French waters as the two countries slid towards war.  That idea has been given ballast by a 1693 diary entry made by Hooke, when Halley and business partner Thomas Jett were engaged in a salvage operation, that “Hally and Jed [were] Spys”. 
Now I have to admit that I’m far from indifferent to this notion of Halley as a secret agent but, like Alan Cook, I’m not wholly convinced by the idea in respect to his present voyage: the Admiralty instructions clearly refer to publishing Halley’s information and they express a concern with the safety of traders of all nations operating in the Channel.
That said, Halley’s earlier surveying activities do seem rather surprising, for example, he was apparently surveying the Thames approaches in early 1689, during the politically-sensitive aftermath of the so-called Glorious Revolution. I’ve started to trawl through the government archives to see if I can unearth anything that indicates whether he was ever employed on intelligence work, but I’ve encountered nothing as yet – though I’ll be sure to reveal such state secrets here if I do!
 National Archives, ADM 2/27, pp 131-2.
 See Cook, Edmond Halley: Charting the Heavens and the Seas (Oxford, 1998) pp 285-6, but note that Cook refers to a published mistranscription of Hooke’s remark.
 Hooke, Diary, 24 March 1693, British Library, Sloane MS 4024.