Cool down your E46 M3 water pump

In this DIY we’ll be going over the procedures for a cooling system overhaul for the E46 M3 water pump which includes thermostat, coolant sensor, fan clutch, and coolant flush.

In our Ultimate E46 M3 Maintenance Guide, we recommend doing the cooling refresh as part of the 100k “Refresh” maintenance. Although we say you can “wait it out” for some of the maintenance jobs on the E46 M3, this is one you should do right away. Even as early as every 75k miles. If your cooling system goes out, you might blow your head gasket or even worse warp your head. Don’t let a surprise water pump failure pull you off the road.

The most common issue with the cooling is the E46 M3 water pump thermostat being stuck in the open position. Although it’s not detrimental to your engine, it may be a sign of failure to come. Make sure to get codes read and diagnose exactly the problem if any. Like any car, the hardest part about predicting when the water pump is going out is, you can’t.

If you have a Engine Coolant Temperature Plausibility or Coolant Temperature Below Thermostat Regulating Temperature error code and it’s been around 75k+ miles since the last water pump and/or thermostat replacement, I would suggest you replace (and bookmark this page) as soon as possible.

Disclaimer: This DIY does require you to lift your car so please use proper tools and follow all safety procedures if you choose to attempt. This guide is for your reference only. We are not liable for any damages or injuries that result from this guide.

Tools Required

E46 M3 Water Pump & Thermostat DIY

  • Jack + two (2) jack stands
  • 8mm socket
  • 10mm socket
  • 13mm socket
  • 16mm socket
  • T25 torx bit
  • 8mm hex bit
  • Ratchet + extensions
  • Torque wrench
  • 32mm wrench
  • Water pump locking tool (001170SCH01A)
  • Needle nose pliers
  • Flat head screwdriver

Parts and Supplies Required

E46 M3 Water Pump & Thermostat DIY

Note: there are 2 main coolant sensors. One is the auxiliary fan switch sensor which is the more common issue, located on the radiator hose. Some people experience leaks which can be easily fixed by replacing the o-ring. The other sensor is the coolant/oil temperature sensor which is used for cluster information. This is found behind the water pump. I decided to only replace the auxiliary fan switch sensor in this guide.

You can view the entire product parts list for which I’ve used here at the ECS Wish List – E46 M3 Cooling.

Directions

1. Jack up the car

1.1, straighten your wheel and use the center jack point to lift the front.

1.2, place 2 jack stands to keep the front of the car lifted.

1.3, use jack or tire as an emergency backup support.

1.4, remove plastic under tray located underneath the car. There are seven 8mm hex screws total.

E46 M3 Water Pump & Thermostat DIY

2. Remove intake

2.1, open your hood and look for the plastic intake duct.

2.2, remove intake duct. There are 4 push pins holding it in. Use needle nose pliers to remove pins.

E46 M3 Water Pump DIY Guide

2.3, remove the intake elbow by unscrewing the c-clamp. I used a flat head screwdriver to loosen the clamp. Don’t remove the intake just yet, unplug the MAF sensor first.

E46 M3 Water Pump DIY Guide

2.4, remove MAF sensor. There are 2 push clips that hold it down. Wiggle carefully.

E46 M3 Water Pump DIY Guide

2.5, remove intake. Unclip the two metal clips on the right side of the air box. Now the intake should come off.

E46 M3 Water Pump DIY Guide

2.6, unplug the two plugs in the headlight ballast. Then remove cover to access 3 bolts. Use a 10mm socket with an extension to remove.

E46 M3 Water Pump DIY Guide

2.7, set aside ballast and remove bottom intake box. Wiggle carefully.

E46 M3 Water Pump DIY Guide

3. Remove radiator shroud and fan

3.1, remove the 3 push pins holding the shield. There is one on top directly center, one driver and one passenger. Remove using pliers. I don’t have pictures of the passenger side of the shield because I don’t run that. Below is a picture of the driver side shield.

E46 M3 Water Pump DIY Guide

3.2, there are a total of four T25 torx screws (one on each corner) and 2 plugs on the passenger side of the radiator/shroud. Unplug cables first, then remove the four screws. The passenger side top torx screw (pictured below) is longer than the others. Tape up plugs and set aside.

E46 M3 Water Pump DIY Guide

E46 M3 Water Pump DIY Guide

3.3, remove passenger side lower screw.

E46 M3 Water Pump DIY Guide

3.4, remove driver side lower screw.

E46 M3 Water Pump DIY Guide

3.5, remove driver side top screw. There is also one little latch hooked on the heat shield. It should pop off with a little bit of wiggling.

E46 M3 Water Pump DIY Guide

3.6, remove fan using the E46 M3 water pump locking tool (001170SCH01A) and a 32mm wrench. The fan clutch nut is reverse threaded. Lock in the water pump pulley and unscrew using the 32mm wrench. Spin the fan to unscrew a little faster, but make sure you don’t let the fan drop.

4. Remove belts

4.1, remove A/C belt using a 16mm socket with a small extension. The tension nut is not to unscrew, but a lever to loosen tension. Have a friend loosen the tension to remove belt. Pictured below is the main E46 M3 water pump/alternator belt (longer) on the right and the A/C belt on the left.

E46 M3 Water Pump DIY Guide

E46 M3 Water Pump DIY Guide

4.3, remove the water pump/alternator belt. Similar to the A/C belt, use a 8mm hex bit to loosen tension to remove the belt. Use the image below to remember orientation.

E46 M3 Water Pump DIY Guide

5. Partial drain coolant

5.1, remove the coolant temperature plug and sensor, plug first. The plug sits on top of the sensor with a metal retaining clip. The sensor is clipped on to the radiator hose with 2 side clips.

E46 M3 Water Pump DIY Guide

5.2, leave a bucket below the car to catch coolant as it drains. Leave the bucket underneath as you’ll need to catch more fluid in the next steps.

E46 M3 Water Pump DIY Guide

5.3, replace auxiliary fan switch sensor if needed. You can see the old sensor on the left with a deformed o-ring and a lot of gunk on the sensor. If you plan on replacing wait until the end when you put everything back together. You’re going to need to leave the radiator hose open to drain even more.

E46 M3 Water Pump DIY Guide

6. Accessing the E46 M3 water pump

6.1, remove the water pump pulley by removing four 10mm hex bolts.

E46 M3 Water Pump DIY Guide

E46 M3 Water Pump DIY Guide

6.2, unclip plug and wire on thermostat housing.

E46 M3 Water Pump DIY Guide

E46 M3 Water Pump DIY Guide

6.3, remove thermostat housing bracket by removing three 10mm hex bolts with an extension.

E46 M3 Water Pump DIY Guide

6.4, remove upper and lower radiator hose from thermostat housing. My radiator hoses were partially melted to the housing tubes so I had to use a flat head to pry around the edges. Be careful if you do this because you may rip the hose. Use a flat head to loosen c-clamp on upper and lower radiator hoses.

E46 M3 Water Pump DIY Guide

E46 M3 Water Pump DIY Guide

6.5, now this is the tricky part! Remove the thermostat housing by pulling up and out. You have very little wiggle room since the thermostat is lodged inside the pump and housing. I had to use needle nose pliers to grab the thermostat and dislodge it from the housing. I definitely damaged the thermostat, but I’m replacing it so it didn’t matter. Once it was dislodged into 2-pieces, there was wiggle room to remove. I will warn you, even after dislodging it’s a PITA to remove. Below is a picture of the thermostat “lodged” into the housing.

E46 M3 Water Pump DIY Guide

E46 M3 Water Pump DIY Guide

6.6, here it is removed. The E46 M3 water pump exposed!

UPDATE: this is a good time to check your VANOS chain guide tensioner as some people experience the bolt coming loose. It’s the hex bolt just left of the water pump in the picture below. Thanks to Max V. for that tip!

E46 M3 Water Pump DIY Guide

6.7, now we need to remove the water pump. There are five 10mm hex bolts holding this sucker in. The very bottom one is the hardest to reach. Careful when pulling the water pump out as it’s connected to 2 black metal tubes. Once this is out, now we can start to do a coolant flush, if you decide to, and prep the new water pump and thermostat.

E46 M3 Water Pump DIY Guide

7. Drain and flush remaining coolant

7.1, locate this cylinder underneath the passenger side of the car, directly above the power steering high pressure hose. Behind the cylinder is a engine block coolant drain plug that we need to get to. On the left side of the cylinder is a 10mm bolt to clamp the cylinder. Remove bolt to swing open left door. The door might be stuck to the cylinder. If so use a flat head to pry open door.

E46 M3 Water Pump DIY Guide

7.2, tuck the cylinder away from the coolant drain spray area and remove the bolt using a 13mm socket with an extension. Coolant will drain out, a lot! Get a catch bucket ready.

E46 M3 Water Pump DIY Guide

E46 M3 Water Pump DIY Guide

7.3, with the engine block coolant plug open, you can flush out your coolant using a hose. You can feed the lower and upper radiator to flush those areas as well. After the system is flushed, plug the engine block coolant plug back in using a new engine block coolant crush washer (07119963200). Torque to 18 ft-lbs. Then, install the cylinder back on.

E46 M3 Water Pump DIY Guide

8. Prep new E46 M3 water pump for install

8.1, install new water pump O-rings (11537830712) on black water pump connecting pipes.

E46 M3 Water Pump DIY Guide

8.2, install new water pump steel gasket (11517831099) on new water pump (11517838159).

E46 M3 Water Pump DIY Guide

8.3, for the O-rings I dipped it in dish wash soap to lubricate for easy install. During installation of your water pump and thermostat housing, your O-rings, especially the large water pump O-ring, may move during the install. Make sure they’re lubricated a little bit so they don’t fall out of position.

E46 M3 Water Pump DIY Guide

8.4, find your water pump bolts and clean the threads for the re-install. Clean them good cause they’re going to require torquing.

E46 M3 Water Pump DIY Guide

8.5, now you’re ready to install the new E46 M3 water pump. Make sure the steel gasket is seated properly and install the water pump back in. Watch out for the 2 black water pump connecting pipes as they should be reinserted properly.

8.6, install the five 10mm bolts back in to the water pump and torque to 7 ft-lbs.

8.7, install new thermostat O-ring (11531318402) on water pump. Lubricate this O-ring before thermostat housing install. (read notes on step 8.3)

E46 M3 Water Pump DIY Guide

8.8, clean up the thermostat housing using Scotch-Brite pad. I’ve seen leaks happen after E46 M3 water pump installations and it is due to bad gaskets or gunk creating improper sealing of the water pump connecting pipes. Make sure you try to get the lip of the thermostat housing and every single O-ring surface free of any gunk.

E46 M3 Water Pump DIY Guide

8.9, install new water pump O-ring (11537830709) on thermostat housing.

E46 M3 Water Pump DIY Guide

8.10, get new thermostat (11531318274) and install thermostat housing back on. Use knowledge from step 6.5 for installation notes. Reconnect lower and upper radiator hose.

E46 M3 Water Pump DIY Guide

8.11, install the thermostat housing bracket back on with three 10mm hex bolts and torque to 7 ft-lbs. Once again, make sure threads are clean.

E46 M3 Water Pump DIY Guide

8.12, install water pump pulley using four 10mm hex bolts and torque to 7 ft-lbs. Use either a screw driver or specialty tool to hold pulley in place.

E46 M3 Water Pump DIY Guide

8.13, reinstall auxiliary fan switch sensor (13621433077) to radiator hose.

8.14, reinstall A/C and water pump belts.

9. Install fan clutch and shroud

9.1, I bought a new radiator fan clutch (11527831619) to replace since mine was pretty old. I got a Behr replacement that was 1/3 the price of the OEM and guess what? The BMW OEM part is from Behr.

E46 M3 Water Pump DIY Guide

E46 M3 Water Pump DIY Guide

9.2, refer to steps 3 and 2 to put everything back in order, but leave step 2.2 out for now since you need access to the bleeder valve for the next step.

10. Fill up with coolant and bleed

10.1, make sure everything is back on! Then time to fill up the new coolant. I used distilled water + a bottle of Water Wetter – 12 oz. Read up on this stuff if you’re not familiar. Great alternative to regular coolant 50/50 mix.

E46 M3 Water Pump DIY Guide

E46 M3 Water Pump DIY Guide

10.2, fill up your coolant/water through the expansion tank with the bleeder open. Fill until bleeder valve overflows. I used around 1.8 gallons until I started to see coolant/water overflowing from the bleeder valve.

10.3, once the coolant/water is filled, turn on your engine with the heater running on highest temp and lowest fan speed. You’ll start to hear coolant/water circulate around the system. Leave the engine on and continue to bleed the valve until you don’t see any more bubbles coming out. Warning: do not over tighten bleeder valve!

E46 M3 Water Pump DIY Guide

10.4, once you see a steady stream of coolant/water bleeding from the valve, close the bleeder and top off the expansion tank if necessary.

10.5, reinstall your intake duct and everything else to run your car. Take your car around the block and re-check your coolant levels.

For the next few days, you’re going to need to keep an eye on your engine temperate and coolant/water temperature. You’ll need to check the floor to see if there are any major leaks. If you experience sudden rise in temperate or large puddles on the ground, you’ll need to reinspect the installation procedure to make sure there are no major leaks. If you experience sudden coolant/water loss, you might have a bad seal in the E46 M3 water pump.

I’ve seen it happen before and it was no fun taking everything back apart. It happened to a friend. Otherwise, you got a brand new cooling system and you just saved yourself a lot money by doing it yourself. Feel free to ask me any questions or post photos of your installation in the comments below! Hope this DIY helped.