The Alfa Romeo driver faced the Ferraris of Carlos Sainz and Charles Leclerc for much of the one-hour training session, taking third place with his first attempt, a 1m46.056s.
Leclerc led at the start, with Sainz taking first place, before Bottas degraded the pair, scoring a 1m42.249 with just five minutes to go.
The session ended prematurely after Aston Martin’s Lance Stroll stretched through Copse’s wetlands, losing its back and ended up stranded in the gravel trap.
Hamilton came late in second, 0.5 seconds behind his former teammate, while Sainz and Leclerc finished third and fourth, respectively.
Dark, heavy rain clouds descended on the Northamptonshire circuit before the session, with constant showers causing a slow start to running.
The Mercedes pair, made up of Lewis Hamilton and George Russell, were the first to come out of the pits amidst the cheers of their local audience, while the Ferrari pair made up of Carlos Sainz and Charles Leclerc followed shortly afterwards.
Both the British and Sainz opted for an installation lap and pitted, while Leclerc got the first time of the weekend on the board with a 1m44.769s.
Variable conditions on the 5,891km circuit complicated things for the teams, with the track much wetter around Copse, while the road from Stowe to Hamilton Straight remained largely dry.
Leclerc improved to 1m43.801s on his second attempt, which remained the only one on the time sheet for 10 minutes, before Yuki Tsunoda made a 1m51.373s with his AlphaTauri.
Sebastian Vettel was next on the track, before teammate Lance Stroll placed second, albeit 10 seconds behind Leclerc.
Sainz was next to make a representative lap, with a 1m49s just behind his teammate, before improving to take first place on his second lap with a 1m42.967s.
A brief burst of quick laps saw Kevin Magnussen take Leclerc’s second place to split the Ferraris before Sainz’s second attempt, while the Alfa Romeos shifted third, with Zhou scoring a 1m46.171 before Bottas was a just over 0.1s faster.
The former Mercedes driver then set a 1m43.437s to split the Ferraris, running just under 0.4s ahead of Leclerc in third place.
Less than half of the grid has had time on the board halfway through, and rain has resumed to further complicate paperwork.
Red Bull’s Max Verstappen, who had only made one installation lap with 20 minutes left to finish the clock, was seen chatting with his father Jos in the garage, while Hamilton came out to greet fans.
The seven-time world champion came out on track provisionally with 10 minutes to go, battling a wet Sector 2 and a strong wind against turn 15 to take seventh place with a 1m49.476s, more of Sainz’s 6.5s at the head, before shaving. almost five seconds on his next attempt.
Bottas improved to second to split the Ferraris before taking first place, before much of the field emerged with five minutes to go as conditions improved.
Hamilton’s last run in the second degraded Sainz and Leclerc, but it wasn’t enough to take first place.
Mick Schumacher finished fifth for Haas, with Zhou Guanyu splitting the German and his teammate Kevin Magnussen seventh.
Stroll took eighth place despite his late accident, with Tsunoda and Vettel completing the top 10. The rest of the grid did not record any timed laps.