I'm almost certain it won't harm your engine at all. It might make it misfire a bit until all of the water has been pumped through the system. What it will probably do though is make your fuel tank rust. In my experience some of the rust formed is quite powdery and can block the jets in your carburettor or maybe the injectors if it's a fuel injected model. Having said that though I believe most cars (particularly those which are fuel injected) have quite a fine filter in the fuel line. It might be worth your while checking this out and maybe fitting one yourself. I hope I've managed to help, and not given you any false information .

beaker
12 gig blue
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Marcus 32 gig MKII (various colours) & 30gig MKIIa