check thermo switch (bottom of radiator on the driver side) maybe a bad temp sensor, or it could be a bad relay. if i was you id just run the fan to a switch in the car so you can turn it on and off when ever and you can have the fan on after you turn the car off.
My first Mk2 had the same issue. Learnt alot about these cars with that old girl. Anyways. It can been one or both of 2 things. If the harness doesnt look stock, as alot of them have been repaird and poorly test it for cross grounding.
If everything there looks alright there and the connections look good buy yourself a new thermo temp switch/sensor. Its located on the bottom drivers side of the rad. If your quick with the wrench you can lay a tray under the spill out and get away with only dumping half a beer can or so of coolant. You can buy them good ones cheap. If you live where its hot I sudggest buying a low temp fan switch. This will give you less panic moments watching the temp guage climbing and not hearing the fan kick in.
That depends on a few things. If you just have the single speed fan, a 2 speed fan, if your car is equipped with the run on air temp sensor behind the valve cover and if it works correctly. A lot of the time they don't work after 15 years. Years worth of engine heat and oil like debris ruining the ground. Just another piece of German electronic engineering.
If you pull up to a parking spot and the fan is on it will stay on for a few min at tops. If you have a 2 speed fan it should kick onto the high speed. More or less to prevent hot spots in the rad. If it turns on after you key off the car its because the run on air temp sensor is telling the car "Oi its hot in here and there isn't any air flow anymore flush this hot air out!"
A comfortable Mk2 temp is in about the middle of the guage on the dash. Obviously it goes down with air flow. If it creeps up then the fan should kick on. If you have a low temp thermo switch installed already or a bigger rad it may only get to half way before the fan kicks on.
If its running hot I would check to see that the water system is circulating properly, warm it up and start feeling hoses too and from the rad and the pump. Most times the thermostat fails in the open position but I have seen a few fail closed witch can attribute to extra warmth. You may also be getting a false reading from a failing temp sender.
I would change the thermo switch out for the low temp one and get a new temp sender while your at it too see if that changes anything. That will solve your fan issues right there. If it still continues to run hotter than normal you may want to take on cleaning the cooling system out.
Thank you all for the helped in pointing me in the right direction when I have had trouble with my 2003 Jetta. Hopefully some of you can find a remedy to this issue by reading my story below. I will be posting my story on the other VW forums as well.
Here it goes: Vehicle: 2003 Jetta 2.0L AVH engine. Problem: Cooling fans operate when vehicle is cold and continue to run even after the engine has been turned off run for about 15 minutes. In order to eliminate a shop or VW dealer (VWD) for wanting to replace the most common items I replaced the fan control module (FCM - tried two one from Amazon and one from RockAuto - URO parts), the cooling fans, radiator mounted coolant temperature sensor, and the A/C cutoff switch. I also checked all the fuses, the fuse box on top of the battery. I figured I am better off spending $100 for a cooling fan unit and install it my self instead of being billed roughly $400 - $500 for having the VWD do it. Preface: At the end of the Chicago winter I had a coolant leak coming from the engine mounted coolant temperature sensor. I waited a month for more pleasant weather to change it. The part cost about $16 plus I paid for an o-ring because I was not sure if the Beck & Arnley part came with an o-ring (which it did).
The remedy: The diagnosis from the VWD was a bad 14 pin connecter which they stated three of the wires were corroded and bent and not making contact. Their claim that this partially caused by a coolant leak, from coolant that made its way down to the connector. I don't know how much creedance to put in to this but changing the plug harness was the remedy. Upon fixing the problem the VWD stated that the installed FCM had gone bad due to a short created by wiring problem. To remedy this they installed a FCM from their inventory and problem solved. I was given an option to bring in my own new FCM which I did because when I did my search for an FCM I called another VW dearship and was quoted $357.00. I did order one from Pelican Parts (Amazon has them as well). I was going to order another third party generic FCM, but had read that some are only good for a month or two before they fail (these are in the $16 to $35 range). I did bite the bullet and ordered a Stribel brand for $105. Stribel is first tier supplier for this part to VW (been there done that with MAF sensor - Pierburg is the better part). In the end I did provide my own FCM which saved me $250 from the total bill. The VWD wanted to replace the alternator wiring harness and fuse box on top of the battery which I declined. These parts go for $125 (for both) on Amazon, I think I can handle replacing those.
Epilogue: I spent weekend after weekend for five months until I took it to the VWD. It was not cheap to have it fixed but I do give them credit for working with me on the FCM unit. For all of you that can't get this resolved and have come up with dead ends - this might your problem. Good Luck!