Thanks to the partnership between Ford and Mazda at the time, the CX-9 uses the 3.5-liter and 3.7-liter Ford V6 gas engines from the Cyclone family (dubbed the Mazda MZI V6 for use in Mazda vehicles). These are used in a multitude of other Ford products such as the F-150 and Transit van. In the CX-9, the engine is fitted transversely in the engine compartment and for such installations, Ford has relocated the water pump from outside the engine to inside the V of the V6 and behind the timing cover due to space constraints. It is driven by the timing chain and difficult to get to. Several owners have complained about a failing water pump, which is one of the most common Mazda CX-9 engine problems.
When the water pump fails, it usually starts to leak coolant to the outside through the pump's weep hole. However, in more serious cases and at higher mileages, its internal seals and bearings break down and it leaks coolant into the engine oil. If not caught early, this can result in terminal engine damage due to the loss of coolant and resultant overheating, as well as the loss of the oil's lubrication ability due to it being contaminated with coolant. This problem is usually related to high-mileage cars and it's difficult to diagnose due to the hidden location of the water pump. The more rudimentary intake-cam-only iVCT variable-valve-timing system in the 3.5 and 3.7 V6s used during the CX-9's life is quite reliable - more so than Ford's Ti-VCT system on both cams used in some Fords like the Mustang and F-150. Ironically, these Ti-VCT-equipped engines have more reliable water pumps. You can't have it both ways, it seems…
What you are probably going to have to deal with sooner or later is carbon buildup on the backs of the intake valves, because the Cyclone was a direct-injection engine during the time it was used in the CX-9. Direct-injection engines lack manifold injectors to keep the intake valves clean, so oil droplets sucked in from the crankcase via the positive-crankcase-ventilation (PCV) system get deposited on the backs of the intake valves, hardening and building up over time until the buildup causes poor running, bad fuel consumption, and misfiring. Cleaning the valves is an invasive job requiring the cylinder head(s) to be stripped.
Lastly, the 3.7's ignition coils can start failing earlier than the typical 150,000 miles one might expect from such parts, but this is neither serious nor expensive to fix.
Mileage: Water pumps fail between 80,000 and 120,000 miles. Ignition coils start failing from 70,000 to 100,000 miles. Carbon buildup on the backs of the intake valves can start to affect the engine's operation from around 70,000 to 100,000 miles.
Cost: Replacing the water pump before any damage occurs costs between $800 and $1,800. Replacing the entire engine with a used one will cost as much as $4,000 and a new one, over $5,200. Ignition coils cost at most $40 apiece and you can replace them easily yourself. Having all of them replaced at a dealer might cost you up to $700. Walnut blasting the intake valves can cost up to $600 in labor (no parts needed).
How to spot: You can't really spot the water-pump problem unless you spot a visible leak early, but it's worth checking the service record to see whether it has been done. If not, it's worth doing as soon as possible. Spending $1,200 is much better than spending $4,000 on a used engine. Open the oil cap and if the oil appears milky, coolant has already found its way into the oil. Oily and mud-like residue in the cooling system means the same thing. There is likely to be visible leaking to the outside, overheating, and even clunking or rattling noises from an already-damaged engine. Failing ignition coils will cause rough running, misfires, and stuttering - and will trigger the Check Engine light. Worn ignition coils will also cause poor running, rough idling, a loss of power, and misfires, while the symptoms for excessive carbon buildup on the intake valves are quite similar, so have the vehicle inspected to see what the problem is before you spend money.