[Update] OP has idicated that this answers his question. I leave the others below, in case they are of any use to others in future.
Valentina Studio Pro includes a visual SQL query builder and you can use most of its abilities within the free Valentina Studio on Windows, Linux and Mac OS X.
FlySpeed SQL Query has both a free, and a paid for ($34.99) version. It looks just like NaviCat and can run in Linux using Wine.
Easy Query BUilder is similar, and free. It doesn't mention Linux, but should be worth trying with Wine.
Also, read https://www.quora.com/What-are-some-good-visual-SQL-query-builders and do some Googling. Could you pelase help us by posting here what you decide to use? Thanks