3 days in Istanbul?

I would try the Arasta Bazaar over the Grand Bazaar, it's more local/ less touristy and more accessible/smaller. Bazaars are not typically hookah places per se, you can go to a hookah bar for that. I would recommend going to one around on the of the universities or Istiklal Street versus the Old City, which is more conservative. I recall one in the Tophane area (near that metro stop, but you can Google and find them (I would avoid the all-male ones, that's why I said go to less conservative parts of the city where there's more intermixing of the sexes). Three days is not a lot, I would not overestimate what you can see - I spent almost a whole day in Topkapi Palace, including some wind down time for a leisurely meal.

You may want to rethink the plan to smoke hookah. In Egypt, the shisha (hookah) bars have been closed for many months because of the Covid-19 pandemic. Numerous health organizations, including The WHO, have issued statements declaring that shared smoking increases the transmission of Covid-19, and the water pipes not being cleaned extremely thoroughly between smokers also increases the risk of transmission. Whether or not the Turkish hookah bars are open, you may want to do your own research and carefully consider whether smoking is worth the risk at this time. Also: I loved traipsing around the Grand Bazaar on my own for several hours, four years ago. I found that Rick's "Istanbul" guidebook was extremely helpful there. He lays out some suggested paths to take through the bazaar, and led me to a couple of delightful untouristed areas and cafes.

Yes, the grand bazaar is fairly close to Hagia Sofia. I think it is worth a stroll through, but I didn't spend a lot of time there (as I wasn't interested in shopping). You will not run out of things to do in 3 days. Here are some suggestions (with caveat that they're based on a pre-Covid trip a few years ago).
Hagia Sofia and Blue Mosque are indeed must-sees. There are lots of other worthwhile mosques, including the Sulemaniye up the hill, and various smaller ones -- but you won't have time to see them all, that would be like trying to see every church in Rome. Try to do at least one other one beside the big 2, though.
Allow at least half a day for Topkapi, it's a big complex -- more if you add the nearby Archeology Museum, which is good.
Near Hagia Sofia, the underground cistern is really cool, as is the Mosaic Museum. Both very worthwhile, but won't take a lot of time. The Turkish and Islamic Arts museum gets good reviews but I didn't see it as it was closed for renovation when I was there.
The main tourist attractions are clustered in the Sultanamet area, where you'll probably stay (which makes sense), but make a point of not spending all your time there. The more modern commercial area along Istiklal St. across the Golden Horn is an interesting contrast, and less touristy.
Take a stroll across the Galata bridge, and enjoy a grilled fish sandwich and beverage at one of the little restaurants under it while taking in the view.
Get out on the water! Options range from a full day cruise to the ordinary ferry over to Asia and back, but a good middle ground is the "Turyol" excursion boat, frequent departures for a 90 minute cruise up to the Bosphorus bridge area and back -- beautiful views, very relaxing, not expensive. Their dock is near Galata bridge.
You don't need to get up early to record the call to prayer (although it will likely get you up early if your hotel is anywhere near a mosque), as it happens 5 times a day. I was in Egypt last month and the first one was at about 4 am, the last one about 6:30 pm. The exact times vary though, depending on your geographic location and the time of year. A quick web search will tell you exactly when it will be in Istanbul on the days you will be there.

Google "prayer times in Istanbul" for your dates. The call to prayer is heard a few minutes before every prayer time. You'll hear it throughout the city. If there are a couple of mosques near you, you may hear an echo effect, as they don't necessarily synchronize.

When planning your day, take into account that all mosques are closed to visitors during prayers. They will usher visitors out 15-30 minutes before prayers and reopen to visitors a few minutes after prayers are concluded. One more reason to know the prayer times in Istanbul ahead of time. Maybe someone knows whether the Hagia Sofia is now an active mosque. There's been a movement to return it to mosque status in the past 3-4 years, but there were hurdles.

The Spice Bazaar is super crowded on Sundays, when other places are closed. If you want to buy, the stalls on the periphery are cheaper than the ones inside. Taste all the flavors of Turkish delight (lokum) before you buy. Very delicious and they vacuum pack it for travel. At the airport it's triple the price.

I don't know where you live. On my visit to the US this year, I saw hookah bars in Foster City CA and Chicago IL. There could be one near you.

I was in Istanbul in May this year and the interior of the blue mosque was under renovation. A lot of the area are closed off to the public and there is nothing to see of the previous magnificence. All the tiles from the walls were removed and I think it will be like this for another 2 years. I went to the Sulimaniye mosque instead which was lovely in a different way.
On the way to the S. Mosque you walk pass the Grand Bazaar and you can pop in there then. The Basilica Cistern was also closed for renovation and may still be when you're there.
The Topkapi Palace can take a couple hours and you can do that, the hagia sofia and the blue mosque (such as it is) in a day with time left over.
You will hear the call to prayer 5 times a day. We recorded the one around midday, sitting near the museum of Turkish and Islamic Art, which is worth a visit. You can do a Bosporus cruise if you have time and also a visit to the Galata Tower.
Hope this helps!

Without a doubt, taking a cruise on the Bosphorus was one of my best travel experiences ever. I just did a normal local route (not the tourist one) and it was still fantastic. Also, if you have time, consider taking a ferry over to the Asia side - Kadikoy is a great neighborhood with lots of small markets and good places to eat (Ciya Sofrasi, etc)

I just showed up to the pier to find the cruise, I didn't look up any reviews ahead of time. Most of the people on my ship looked like locals getting off at various stops. The tourist cruises usually dump people off at some fortress in the north of the Bosphorus for a few hours so they can dine at some specified fish restaurant, I avoided that one. Just be aware that (hardly) no one will speak English so you have to just wing it.

Yes, the Archeological Museum and especially the Tiled Kiosk (part fo the museum) were excellent. Also, there are TONS of mosques in Istanbul, you don't have to go to the Blue Mosque. I liked the Rüstem Pasha Mosque by the Spice Market (gorgeous tiles). Anything designed by Sinan will be worth seeing (https://en.wikipedia.org/wiki/List_of_Friday_mosques_designed_by_Mimar_Sinan)

I am headed to Istanbul today. (Woohoo!). It's one of my favorite cities.

A few recommendations and tips:

• Plan to spend at least a day in Sultanahmet. Hagia Sophia, Topkapi, and the Basilica Cistern are must-sees, and there is a plethora of museums in the area. The Archaeological Museum especially interesting. Budget half a day for Topkapi. Not only is it large, but you will also spend a lot of time waiting in line to get into the little rooms with all of the jewels and armaments.

• The Grand Bazaar is an easy 15 minute walk from Sultanahmet. The Grand Bazaar is touristy. You need to see it, but there are better places to shop. Because several of the other well-known mosques are under renovation, you might want to make some time to visit the Suleymaniye Mosque, which is not far from the Grand Bazaar.

• I highly recommend a Bosphorus cruise. You can take the public ferry, a private cruise, or Turyol (private but cheap). It depends on your budget and preferences.

• Istiklal Street is worth a stroll.

• Never trust taxis around Sultanahmet. 90% of them are a ripoff. ( I know from experience.) If you need a taxi, get one from your hotel.

• Streetcars are excellent, cheap, and will get you to just about anywhere you need to go.

• If you like to be pampered, you might consider visiting a hamam. The Aya Sofia Hamam and the Cagaloglu hamam, both in Sultanahmet, are two of the more luxurious ones.

A few updates (as far as I can tell):

• The Blue Mosque is under renovation. It's open, but you won't be able to see much. A temporary ceiling blocks the view.

• Rustem Pasha Mosque is also under renovation and is not open to the public.

• Chora Museum/Mosque is also closed for renovation.

Hello from Wisconsin,
Get a fish sandwich near the main bridge between Sultanahmet and Galata. The sandwiches are available on the ground, near the water on the north side of each end of the bridge. The Galata side is the fish market and the sandwiches are a bit more real. With a glass of lemonade...fantastic.

Kariye Mosque is definitely worth the time and effort to get there. The mosaics are spectacular.. Plus, while you are there, the Wall of Theodosius is near by. Istanbul is protected on three sides by water, the land side has this amazing wall from the time of Theodosius. Remodeled and updated periodically since the 5th century.

Kucuk Ayasofia. The little Aya Sofia. Getting here will take you through some nice old neighborhoods. The church, now mosque, is from the 6th Century. The door was open when ever we went to visit. It is an active mosque so please be reverent, don't enter if it is being used.

The Arkeological Museum. My goodness! The things they have laying around outside the museum because they aren't good enough to get inside...just one of those items would cause a stir if it toured Wisconsin.

See the area between and around Aya Sofia and the Blue Mosque at night.

The Hippodrome is right in the neighborhood of the Blue Mosque.

This a very old city by western European standards and you can't runout of things to see.

wayne iNWI

Basilica cistern is still closed for renovations, but you can go to Theodocian (serefiye cistern).
Blue mosque can be skipped as you cant see much in there because of renovation works
Hagia sophia is open 24/7 but just for information it is close in the morning for cleaning from 8:00am to 9:00-9:30am.
Rustempasa, suleymaniye and fatih mosques are definetly the ones you should try to see.
I also dont recomend hookah bars because of covid.

Arasta Bazaar is a JOKE comparing with Grand Bazaar!
All of those places are close to each other so u will have enough time to see all of them in 3 days. Plus you can see Kadikoy and Uskudar in Asian side in these three days too.
Dont miss seeing Suleymaniye Mosque. Its better than overrrated Blue Mosque with better view of the city!
Try to see Eyup Sultan mosque , Ortakoy and Besiktas too. You can do in three days easily!