Fungi and other microorganisms can survive and multiply in diesel fuel if water is present. The fungi can be present in any part of the fuel handling system. These fungi grow into long strings and will form into large globules. The growths appear slimy and are usually black, green, or brown. The fungi may grow anywhere in the fuel but are most plentiful where diesel fuel and water meet. As the fuel is agitated, when service station tanks are being filled, fungi are distributed throughout the tank and may be pumped into a vehicle.

Fungi use the fuel as their main energy supply and need only trace amounts of water and minerals. As they grow and multiply, they change fuel into water, sludge, acids, and products of metabolism. The most common symptom is fuel filter plugging; however, various metal components including the fuel sending unit, pipes, fuel injectors, and injection pump can corrode.

Caution: Avoid physical contact with the biocides in order to avoid personal injury.

If fungi have caused fuel system contamination, use a diesel fuel biocide to sterilize the fuel system. Do not exceed the dosage recommended on the label. Discontinue the use of a biocide when towing a trailer. It is permissible to have biocide in the fuel when starting to tow, but do not add any biocide while towing.

Steam cleaning may be necessary if most of the fungus growth cannot be removed with biocides.

The presence of water or gasoline in diesel fuel may also cause injection pump and nozzle damage.

This procedure checks for the presence of water and gasoline in diesel fuel that may cause injection pump and nozzle damage.

Remove and inspect the fuel filter element.

1. Disconnect the negative battery. Refer to Battery Negative Cable Disconnection and Connection .
2. Remove the sending unit. Refer to Fuel Sender Assembly Replacement .
3. Inspect the fuel tank and the fuel sender for rust, fungi or bacteria. If there is rust, replace the rusted components.
4. Clean the inside of the fuel tank and the fuel sender with hot water.
5. Use compressed air in order to dry the fuel tank and the fuel sender.
6. Disconnect the ends of the following lines:

•	The fuel filter inlet line (both ends)

•	The transfer pump pressure line and suction line (if applicable)

•	The fuel filter outlet line (both ends)

•	The fuel filter drain

•	The fuel return line (both ends)

7. Inspect each of the pipes and lines.
8. Replace any rusted pipes.
9. Clean the inside of the fuel filter housing.
10. Dry the fuel filter housing with compressed air.
11. Dry the inside of each line with low pressure air.
12. Remove the ignition 1 relay from the underhood relay center.
13. Install a new fuel filter. Refer to Fuel Filter Replacement .
14. Install the sending unit. Refer to Fuel Sender Assembly Replacement .
15. Add clean diesel fuel to the primary tank until the tank is ¼ full.
16. Reconnect the following lines:

•	The fuel filter inlet line

•	The fuel filter outlet line

•	The transfer pump pressure and suction (both ends) lines

•	The fuel return line (tank end)

17. Connect the fuel filter drain to a line that flows into a clean metal container.
18. Connect the batteries.
19. Operate the fuel system hand primer at the fuel filter until clean fuel flows from the fuel filter drain into a metal container.
20. Close the fuel filter drain and remove the bleeder hose.
21. Install a hose on the fuel return line near the glow plug relay, and insert other end into a 7.6 liters (2 gallon) metal container.
22. Crank the engine for 30 second time intervals, with 1 minute cool-down periods. Continue until 3.8 liters (1 gallon) of fuel has passed into the container.
23. Connect the fuel return line.
24. Install the ignition 1 relay in the underhood relay center.
25. Start and run the engine.
26. Stop the engine.
27. Clean any fuel spillage from the engine.
28. Fill the fuel tank and add a biocide, if needed.

1. Drain the fuel tank.
2. Fill the fuel tank to ¼ full.
3. Unplug the crankshaft position (CKP) sensor.
4. Loosen the fuel filter drain and connect the filter to a hose that flows into a metal container.
5. Operate the fuel system hand primer at the fuel filter until clean fuel flows from the fuel filter drain into the metal container.
6. Hand tighten the fuel filter drain and disconnect the hose.
7. Install a hose on the fuel return line near the glow plug relay, and insert the other end into a 7.6 liters (2 gallon) metal container.
8. Crank the engine for 15 second time intervals, with 1 minute cool-down periods. Continue until 3.8 liters (1 gallon) of fuel has passed into the container.
9. Reconnect the fuel return line.
10. Plug in the CKP sensor.
11. Attempt to start and run the engine for 15 minutes. If the engine does not start, operate the hand primer for 30 strokes, or until firm.
12. Stop the engine.
13. Clean any fuel spillage from the engine.
14. Clear the engine of any diagnostic trouble codes (DTCs).

Important: 

1. Disconnect the negative battery cable. Refer to Battery Negative Cable Disconnection and Connection .
2. Drain the fuel tank. Refer to Fuel Tank Draining .
3. Remove the fuel sender assembly. Refer to Fuel Sender Assembly Replacement .
4. Inspect the fuel pump strainer. Replace a contaminated strainer and inspect the fuel pump.
5. Inspect the fuel pump inlet for dirt and debris. Replace the fuel pump if you find dirt or debris in the fuel pump inlet.
6. Locate a stand or fixture suitable to support the weight of the fuel tank and water.
7. Turn the in-frame rail fuel tank over so that the modular reservoir assembly opening is facing down.
8. Install side mounted fuel tanks upright and horizontal on stand of fixture and remove the drain plug and set aside for re-installation.

Important: 

•	When flushing the fuel tank, handle the fuel and water mixture as a hazardous material. Handle the fuel and water mixture in accordance with all applicable local, state, and federal laws and regulations.

•	Do not drill any access or drain holes in the fuel tank.

9. Using a high pressure water spray-wand, spray all interior surfaces with clean/non-contaminated water. Be sure to spray all interior tank surfaces including for and aft sections of tank behind baffles, while allowing water to drain out the modular reservoir assembly opening or drain hole. Perform each wash cycle for a minimum of 30 seconds using a minimum of 4 liters (1 gallon) of clean/non-contaminated water.
10. Using a high pressure wand, dry all interior tank surfaces. Tank should be tipped accordingly to facilitate removal of water. Assure pressurized air does not contain any contaminants.
11. Repeat steps 10 and 11 for a total of 3 wash/dry cycles.
12. Hand dry tank surfaces with a white towel to confirm dryness and cleanliness.

Use a non-metallic extension to push the towel beyond tank baffles.

13. If equipped with a fuel drain plug:

•	Remove old sealant from the drain plug male threads and tank drain the female threads.

•	Apply new (.05 mm thick) coat of sealant (P/N 9985253) to the drain plug male threads and tank drain the female threads.

Notice: Refer to Fastener Notice in the Preface section.

•	Install the tank drain plug.

Tighten
Tighten the tank drain plug to 35 N·m (25 lb ft).

14. Install the fuel sender assembly. Refer to Fuel Sender Assembly Replacement .
15. Refill the fuel tank.
16. Install the fuel filler cap.
17. Connect the negative battery cable. Battery Negative Cable Disconnection and Connection .
18. Start engine and inspect for leaks.