Flower of Germany has her in trouble (5)
I believe the answer is:
rhine
'flower of germany' is the definition.
'Rhine' can be an answer for 'flower' (River Rhine, something which flows). I'm unsure of the 'of germany' bit.
'her in trouble' is the wordplay.
'trouble' indicates anagramming the letters.
'her'+'in'='herin'
'herin' anagrammed gives 'RHINE'.
'has' is the link.
Can you help me to learn more?
(Other definitions for rhine that I've seen before include "water" , "River of Cologne" , "fed by 8 [RHUR]" , "River flowing from Switzerland, through Germany, to the North Sea" , "River, rising in Switzerland and flowing into the North Sea" .)