A number of different factors can effect how long a query takes to run. Certainly the size of a table and the complexity of the query play a big role. Locking can really slow a query down by making it wait to get started. A series of competing queries that induce table locking can grind things to a halt.
If you don't want queries in a particular connection being allowed to wait or run too long, you can set a timeout.
set statement_timeout to '500';That will ensure that any statement run in that connection will be terminated if it takes longer than 500ms.
You can also specify a unit:
set statement_timeout to '15s';That will enforce statement timeout of 15 seconds.
See the docs for more details.