In the following sentence, is there any ambiguity about the pronoun "they"? they refers to pumps, is it clear?
The current flows into the electric motors that drive the pumps that expel water when they contract.
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In theory, yes there is a little ambiguity, since your sentence mentions two different "things", i.e. 'pumps' and 'electric motors', either of which could be the subject.
In reality, the context makes it fairly obvious in this case that it refers to 'pumps' since 'motors' are unlikely to 'contract'.