Well, let's look at what it says in the Baldur's Gate entry in the FRCS.
"depends on the trade passing through its ports and gates"
"city's population is believed to have long ago surpassed even Waterdeep's"
"contains an active and organized thieves guild, powerful merchants with questionable ethics, and influential cults and secret societies both malignant and benign".
All power groups maintained under a delicate balance by ex-mercenaries, the Flaming Fist; police, law enforcement, protector.
The city remains neutral in regional politics.
So, what do we have here?
1) A large commercial city that depends on trade. Thus, any sort of threat to commerce is going to put a serious hurt on the place. Piracy, sea/river monsters, or harsh weather along the coast (controlled by some entity), or problems/attacks up-river from Baldur's Gate could hurt shipments. Banditry, bad weather, or bad crops could cause problems for merchants traveling by caravan. Because it's all about trade, then there will be
big problems with smuggling.
The merchants hold a lot of power. So, you could have merchants trying to undercut their rivals with sabotage ("Yes, release these magically enhanced pests into the grain warehouse of my rival, if you please"), cutting corners or covering up bad deals ("Yes, my alchemical leavings are being dumped into the river. Those mutated crocodiles are not my concern.") or ratcheting up their prices so bad that it's causing problems. Not to mention the whole issue of unions (which can cause riots, gang violence, and a slew of assassinations).
The PCs could for instance be hired as guards for a warehouse - and that same night, some flamboyant burglars break in, to steal something very valuable. And during the battle, some exotic creature is let loose from its cage, causing havoc all over the place.
2) Politics. Any city is rife with intrigue (murder mysteries, espionage, backstabbing and backroom deals between the city counsel, nobles, or between (or even from within!) the church). The different city factions are hinged on a delicate balance, that could be disrupted if there is a power vacuum. Add in the practice of not getting involved in regional conflicts, and various regional entities could be fairly sore about Baldur's gate.
3) Regional interests. The book mentions two adventure sites: One of the adventure sites is "Mandorcal's Mansion"; the district was owned by a rival of a tiefling drops dead (his blood drained). 3 days after it's purchased, a mansion stands in an empty lot. Then the owner goes missing, and traps any who come inside; rooms shift, diabolical chants echo, and scenes of butchery unfold before those inside.
There is also a sealed-shut wizards tower underneath the city.
4) Cults/Secret Societies. This can go back to #2, or it can be something entirely different. Far-Realms worshiping occultists, vampire-groupies, or even something benign like the Masons or Stamp Collectors, who might just appear to be the cause of something that they are not responsible for.
5) Typical City Problems. With Baldur's Gate being so big, it's going to have issues like crowd control, disease, sewage/garbage/clean drinking water, housing, etc. While they may sound boring, they're easy to play with (that tenament fire was caused by a slum-lord who wanted to collect insurance on his property, although he had no idea the warlock in 3C had a fiend bound in one of the rooms) or (Local druids are causing serious headaches over the sewage buildup which is killing local wild life, and now they are retorting by herding otyughs into the sewage areas; carrion crawlers are infesting the local garbage dumps). In fact, on that vein,
check out the latest Vicious Venue. Not to mention riots, natural disasters/severely bad weather, bank robberies, etc.
6) Similar to #5: ye olde typical Urban adventure fodder. Thieves Guild plots. Monsters (like wererats) in the sewers. Monsters (dragon, vampire, doppelganger, etc) manipulating some group(s) from the shadows. Intelligent undead or other monsters stalking the streets at night. Murder mysteries. Haunted Houses. Kidnappers capturing people for some nefarious purpose (cult sacrifice, eating them, slave trade, etc).