Some owners have reported BMW E46 throttle body problems, which could be a major issue, considering that later models employed an electronically actuated throttle body to control everything from idle speed to engine response. These issues are usually resolved by cleaning the throttle body of any accumulated gunk, especially on cars with a prior history of PCV problems, but can also be caused by a poor electrical connection between the throttle body and its wiring harness, and could trigger a P0121 and P0123 error codes in the diagnostic system.
The starting system also appears to be largely trouble-free, with the only BMW E46 starter problems to report revolving around the standard-fit anti-theft system. Either the immobilizer control unit or the coded key could go wrong. In the former case, the only solution is to replace the faulty controller, but in the latter case, there's also a possibility that the ignition key simply needs to be reprogrammed. Some owners also report that the crash sensor, located in the main power line next to the battery in the trunk, could malfunction, which will also cause a no-start condition.
Closely linked to the probable immobilizer issue are problems with the BMW E46's central locking, boot lock, and key, which could point to the same control module. However, there is also a well-known problem with the GM5 module behind the glove box, which controls the locking system. This problem can often be repaired by replacing the some relays inside this module, following which it should be working again.
There are also very few complaints about the charging system, with BMW E46 alternator problems usually only occurring due to corrosion in the alternator, or plain old wear and tear on the internal carbon brushes or regulator. BMW E46 battery problems don't appear to be a notable issue, although some electronic components could cause a slow battery drain due to poor earth connections.
The climate control system appears to be quite robust, and BMW E46 AC and heater problems are usually solved by replacing the cabin air filter or ensuring that the airflow control flaps in the HVAC system are working properly. There don't seem to be any design flaws in the cooling hardware, however, so the AC compressor and heat exchangers shouldn't pose any issues.
Problems with the BMW E46's manual gearbox and clutch are few and very far between, and, because these cars didn't employ a limited-slip differential, they generally don't need any attention, apart from an occasional clutch replacement or perhaps repairing a leaking oil seal.
The brakes are another story, with many owners complaining about BMW E46 handbrake problems. However, it usually turns out that the handbrake was never properly adjusted on those problem cars, with very few cases of owners needing to replace any components to get it to work as it should and the rest eventually getting it right after repeated adjustments.
Very few owners mentioned BMW E46 water leak problems, apart from the engine's cooling-system leaks, that is. Body-related water leaks are usually caused by blocked drainage channels in the sunroof assembly or the roof pillars, and cleaning them out is often a massive mission. However, an unchecked leak could eventually lead to electric problems, as some control modules are located in quite vulnerable areas.
BMW E46 sunroof problems have been mentioned by a number of owners, and the problems usually revolve around the sunroof frame's assembly. Either the drive cable stops working or the tilt-sliding mechanism warps, and both of these faults will cause the sunroof to stop working. The worst bit is that it's a big and costly mission to repair, because half of the interior has to be torn-down to gain access. Consequently, many owners simply stop using the sunroof.
There are no body-specific 2000-2005 BMW E46 wagon problems, but convertible owners often have bad luck. BMW E46 convertible problems can range from wiring issues to position switches in the mechanism, and often include some issue or pressure drop with the hydraulic system that operates the roof.