Yes. There's a variety of ways to do this.
Wikimedia uses a heavy-weight approach known as $wgConf. It allows setting up different per-wiki configurations. However, this can be a little confusing to set up, and the documentation for $wgConf is a tad sparse.
Note, if you want to use certain cross wiki extensions (such as Extension:GlobalUsage), you may need to go the $wgConf route.
Another way that is more common in really small cases, is to have three separate directories all containing symlinks to the wiki code, but with each directory containing its own LocalSettings.php.
You can even have just one directory with wiki code, and the LocalSettings.php file, but have an if statement in the LocalSettings.php file. Something like (haven't tried that, so probably made a typo somewhere)
if ($_SERVER['SERVER_NAME'] === 'fr.mywiki.com' ) {
$wgArticlePath = 'blah';
$wgScriptPath = 'blah';
$wgDBName = 'foo;
// and so on
} else if ...
You may also want to read about manual:$wgSharedTables, manual:$IP, and manual:Wiki family