Unusually, Mercedes did not top either Friday practice session - with Red Bull's Max Verstappen and Racing Point's Lance Stroll quickest respectively - with the top of the timesheet rather more closely-matched than has been the case at the start of the 2020 season.
Temperatures hit 35 degrees Celsius during the afternoon at a sun-drenched Silverstone, while the notoriously gusty winds whipped around the old RAF airfield with particular venom to challenge drivers on the fast, flowing circuit all day.
Hamilton was fifth fastest in Practice Two and said: "Quite a difficult day, to be honest.
"It's always windy here, which is actually a good thing about this track that you've got some wind in different directions, but it's made it really tricky today with the car and the balance is not as good as I'd like.
"So we're just going to work on it tonight and try and see if we can figure it out. It's not a disaster but it's definitely been a hard day of driving."
In Practice Two, the six-time world champion and six-time Silverstone victor completed two laps on the quickest soft tyre either side of the Alex Albon-triggered red flag but backed out of the second after running wide at Brooklands.
"We'll work through it," added Hamilton. "We've got great engineers and that's the great thing about this team - we just continue to dive deep into the details and hopefully we'll make some good changes overnight.
"I think it's going to be cooler tomorrow as well."
Team-mate Valtteri Bottas, third fastest in the afternoon session, expected Mercedes to work their way up as conditions cool into Saturday.
"Obviously still work to do, but Practice Two was actually not a bad feeling," said the Finn, who trails Hamilton in the championship by five points.
"The gaps are quite small and normally we are able to make some good steps for the qualifying, so not too worried because the overall feeling is quite good.
"But Racing Point and Red Bull seem quite strong as well. It's going to be completely different conditions tomorrow with quite a lot less track temp and the wind direction is going to change quite a bit, it normally has quite a big effect on this track."
With Lance Stroll finishing quickest for Racing Point ahead of Red Bull's Albon, Hamilton added: "That's great to see close competitors and hopefully tomorrow it's close with us also."
Albon's afternoon crash at Stowe not only ended his participation in the session but disrupted a number of drivers' qualifying simulations, meaning the final timesheet was even more misleading than usual on a Friday.
However, before his accident, Albon had set the second-quickest time and was encouraged by the performance of the RB16 after a difficult Hungarian GP when the car was unbalanced.
"We've definitely made a step as a team. The car feels good and most probably we expected worse, to be honest, coming in to today," said Albon.
"The car was hooked up straight away the first time we drove it in P1, so it's looking good. Obviously I'm sure the Mercs are hiding quite a lot so we'll watch them [on Saturday] but otherwise as a car it feels well balanced. But the weather today is different from what we're going to get tomorrow."
Max Verstappen, who was annoyed to lose time behind Romain Grosjean on what should have been his best lap of the day, agreed: "The car is working a bit better, so happy with that. There are still things you can improve, so we'll work on that, but on the long run it was looking quite decent."