My wife and I have booked 3 days in Bellagio in mid-September. We are looking for advice on how to best spend our time - best activities, great restaurants, things we can't miss. We are up for anything, and would like to make the most of our time there. We will have a car, so getting around will not be a problem.

Park the car and take a boat from Bellagio to Varenna, Menaggio, Tremezzo, back to Bellagio.
Very easy, all a short boat ride from Bellagio.
You can do the triangle all in one day but we like to take our time and enjoy the surroundings so we took a couple of days.

We stayed in Tremezzo for 10 days in September. The weather was beautiful and this was our favorite part of the lake.

Gorgeous gardens and views from:
Varenna….Villa Monestero
Tremezzo….Villa Carlotta
Menaggio….beautiful promenade

The only place we did not like was the city of Como itself, too big and busy.

If you like a fancier lunch dine on the balcony of the Grand Tremezzo Hotel.

BTW, I am envious of your trip. This is a stunning part of the world to explore. Pleas report back when you return.

Dining- walk south along the lake from Melzi Gardens to Loppia- dine at Alle Darsena di Loppia is an excellent place to dine. Also La Barchetta,in Bellagio center.
La Grotta for pizza.
Visit Villa Balbianello , go by ferry to Lecco across the lake, then a short walk or a water taxi to the Villa nearby.

In the hills above Varenna, there is a falconry housed in the ruins of Castello Vezio. You can reach the castle by bus, cab or on foot (steep path, better done downhill). (It's not worth taking the car on the ferry and trying to drive to it.) The birds are released on a schedule. Check with the Info/Tourist Office in Varenna (or Bellagio) for times. Views of the lake from the castle are wonderful.

If you're a fan of cycling (Le Tour, Giro, etc., or just your weekend pedal), you might want to visit the Cycling Museum in the hamlet of Margreglio south of Bellagio. Adjacent to the museum is the Shrine of the Madonna del Ghisallo, the patroness/protector of cyclists. The Tour of Lombardy (mid-October) stops at the chapel every year. This is the only time you'd need the car.

https://www.museodelghisallo.it/en/

Ferry boat across the lake for lunch! We loved the boats around the lake--up to Varenna is a short hop and many prefer that town to Bellagio (we don't).

What everyone wrote, except for the city of Como* (I haven't been there so can't agree or disagree).

Here's my trip report...scroll down to post #15:

https://www.fodors.com/community/europe/turin-spoleto-bologna-and-bellagio-tr-947180/

*Have read about its textile history... an interest?

The Melzi garden is close to Bellagio

https://flic.kr/p/7pds7H
and the villa Carlotta garden is a ferry ride away

https://flic.kr/p/7phk5f

Re: city of Como. It is where the silk factories were located. The lakefront section is a nice medieval quarter if you happen to go to Como.Otherwise it’s a skip. Mid lake is much more scenic, Bellagio, Menaggio, Cadenabbia etc..

we had a car in Bellagio and did not use it.... do you have parking as parking is really very limited. also, getting in and out of bellagio is quite difficult.
We used the boats to get around the lake, and it was a lovely way to get around.

also, I quite like the city of Como. but we only did a short visit.

Having a car in Bellagio is difficult. Hotel Belvedere is one of few places with parking. We only had a car once in four trips there. We used a Como based driver to pick us up from MXP.

Wow! These are all fabulous suggestions! We will definitely park the car and explore the area by boat, and will see where we go from there. Two other questions - any more lunch/dining reccos in Bellagio, or any of the other towns around the lake? And would a day trip to Lugano be worthwhile?

You only have 3 days, and only you can decide whether you want to spend one of those days making a day-trip to Lugano. You won't run out of things to do/see on Lake Como.

Figure out what you want to see on Lake Como, study the ferry timetables to understand how long it takes to get around and what's possible in a day. Pay attention to the time of the last ferry back to Bellagio.

Excellent advice! Thank you!

Lake Lugano has a larger lakefront town. I would not give up any time in Bellagio to go to Lake Lugano. We drove there for lunch when leaving Lake Como which was fine.