Learn German: Das Mehl ist in der Schüssel.

This is because in is a "two-way preposition". When it answers the question "where?" (describing a static location where nothing is changing places), it forces the following noun into the dative case. In the dative case, the feminine article die changes to der.

Is there a rule for the gender of Schüssel? I thought words ending in "-el" were usually masculine.

You have a good memory! Many nouns ending in -el are masculine (like der Löffel for "the spoon" or der Apfel for "the apple"). However, die Schüssel (the bowl) and die Gabel (the fork) are common feminine exceptions that you just have to memorize.

Could I contract in der into a shorter word here?

No. Unlike in dem, which commonly shrinks to im, or in das, which shrinks to ins, the feminine phrase in der cannot be combined into a single word. You always have to write it out.

What if I wanted to say "I am putting the flour into the bowl"? Would it still be in der Schüssel?