The water pump could be considered the achilles heel of the GS. The pump is known to fail and it fails repeatedly on some machines and not on others. The reports of failures also appear to be higher on the F650GS than the G650GS. The most obvious difference between the models is the clutch/water pump casing on the F's. In at least one case replacement of the clutch/water pump casing under warranty solved the problem of the failures. There is discussion with regard to the quality of the seals and the use of alternative seals.Overall the answers are not clear but it is likely to be a combination of the design, cover alignment and seal type.
The BMW maintenance schedules are not clear on when to change coolant, it should be done every two years. When changing coolant ensure the engine is warm, when the engine is cold the thermostat will be closed and may need removal to drain the old coolant. It can be a delicate and painful process releasing the thermostat.
There is a bleeder valve on the RHS of the cylinder for use when changing coolant. Early models have a plastic tube fitting, on later models it may be a torx bolt. Loosen until fluid appears when filling with new coolant, then tighten. Squeeze coolant hoses repeatedly to ensure all air is removed.
BMW have their own coolant standard. There is much discussion about alternatives. This Coolant Info pdf sets out the basics of what is known.
Water pump replacement is relatively straight forward but complicated by the combined clutch/water pump cover which requires draining the coolant as well as the engine oil. The rigid oil line is another complication.
Refer to the manuals for details on water pump replacement. One day when time permits I will add a pdf here.
RG Tooling Ltd UK made an engine case which allows clutch inspection without disturbing the water pump but the costs would be considerable. The G Series has a similar engine case. Water Pump Parts pdf
Standard SealsBMW use FP seals, rated for 0.5 - 1.0 bar
When replacing a water pump it would be advisable to check
the cover alignment and wear on the bearing surface. Wear on
the plastic gears driving the impeller can also be a problem
and the gears are known to break up.
A new shroud and fan was fitted to the 2010 models and is listed as fitting the older GS models.
Info on fan replacement is in the pdf Fan Info pdf
The BMSC/E turns the fan on at 102c, the dash lamp turns on at 118c.
2013+ bikes have a fan relay near the fuse box under the seat
The new fan and shroud fits the earlier models very well.
The original radiator design has two separate mounting tabs spot welded to the top tube. The design was upgraded to a single large bracket spot welded to the top tube. The issue with the two smaller tabs is the load is too great on the top tube and fractures it. The single bracket spreads the load and avoids the stress fractures. (The two mounting locations are the same) It is unclear when the change was made. See the details in the F650.com thread
Rocks can become lodged between the frame down tube and the radiator, if they are not removed they can wear through the alloy of the radiator. The radiator fan can also rub on the radiator. It is worth checking both periodically.
A pdf with radiator chafing and other radiator repair information. Coolant System pdf
Paint inside the junction on the frame can blister and the flakes go
through the cooling system. When changing coolant it is worth
checking and cleaning the inside surfaces.
Note - Coolant Hoses are 22mm ID
The thermostat design is the same as many Euro cars, the return spring
is a stronger spring however. The housing retaining clips can harden
and break. See the f650.com threads in repair links for more detail
Alternative suppliers are in the Thermostat Info pdf
The rigid oil return line on the F Series makes removal of the
left engine covers difficult. The G Series have a relocated oil
return line against the side of the cylinderwhich may fit the
F Series but the starter motor mounting is different.
See Modifications/Other Modifications for information on Radiator Guards.