I have a civic si 2000, and recently i have noticed that the gauge on the dash that indicates the water temperature has been really high.
However it gets high only when im driving around town, it slowly lowers when i drive on the freeway.

I have checked the thermostat physically.
I have jumped the fan to and it does work.
Just now, i had the car idle for ~5-10 minutes, and the fan did turn on, but the temperature gauge on the dash still climbs. (The top hose from the radiator was warm/hot and the bottom hose from the radiator was cool)
I feel like the fan sometimes turns on when the car is hot, and other times it does not run.

*update*
Information I forgot to provide was that approximately six months ago the timing belt and water pump was replaced.

*Update*
The radiator is approximately four months old.

*Update* 03/09/13 look at latest post.

 

Lack of rust does NOT indicate that the thermostat is good. Where did you hear that? Being bathed in coolant constantly I would be curious to see how that was even possible. Change the thermostat.

 

Thermostat replaced but the issue is still not fixed, any other suggestions?

 

Did you bleed the cooling system after installing the new thermostat?

 

OP, are you loosing any coolant?

 

Maybe problem with gauge, until both hose ( upper and lower) become hot ventilator should not be turned on.
Disconnect ECT sensor when engine is off, measure resistance with Ohm meter :
Engine temp.
68F = 2000ohm
104F = 1000ohm
176F = 300ohm
212F = 200ohm

You should have between 200 and 300 ohm when engine reach working temperature ( ventilator turned on)

 

http://www.clubcivic.com/board/showthread.php?t=203345
^^ very similiar problem to this guy
No i did not, but I will definately do that now.
I am losing a bit of coolant
I do not have ohm meter nor do I know what/where the ECT sensor.
I am not sure if this is a strong indicator that the gauge is right, but when the the gauge is high enough, I can feel the engine vibrating (So i would guess the gauge is correct)

**updated the original post**

 

how many miles on the car? when was the last time the water pump was replaced?
my old 96 civic had this same problem, highway was no problem but in town (especialy idling at stop light/sign) would start to over heat.
once you start giving it gas the temp would go down... water pump ended up being bad.

 

Mileage is 150k, the water pump was replaced approximately six months ago.

 

Identify where is the coolant going or leaking. If you can't see any leak, chances are it is leaking past the head gasket. Have it tested.

 

Update: So today I took my car to a shop, the mechanic had some sort of expensive obd2 reader and we found out that when the coolant is ~237F is when the fan would turn on (near H on the temp gauge), but the fan would only stay on until the temperature drops to ~234F.
Another thing he noticed was that even though the fan was on, the ECU never sent the signal to the fan. Came to this conclusion because the obd reader was reading "Rad fan: Off".
Is this a strong indicator that my ecu is broken? Reason I am asking is because I really do not want to waste any more money than needed.
he was also saying that the ecu should have at least turned the fan on at around 215F

 

Interesting thing is that you have embedded ventilator fan control in ECU, in most case is controlled only trough temperature sensor who located at bottom of cooling radiator or near to thermostat. Like I say before, try locate them, measure resistance or just buy new and replace.
Is that problem?

 

why the hell would you keep driving the car when its overheating?? like others have said, thermostat, water pump, bleed the system, find the leak, and figure out why the fan is turning on so late.

not really that hard. how long have you kept the engine running when it was very hot like that? you'd be lucky to not have done a lot of damage.

 

Coolant temp sensor and bleed the sytem