Fresh water essentially where it may breed (4)
I believe the answer is:
newt
'it may breed' is the definition.
The definition suggests a singular noun which matches the answer.
'fresh water essentially' is the wordplay.
'fresh' becomes 'new' (synonyms).
'essentially' indicates the central letters.
The middle of 'water' is 't'.
'new'+'t'='NEWT'
'where' is the link.
(Other definitions for newt that I've seen before include "Amphibious salamander" , "Amphibian - a Ken Livingstone pet?" , "Scientist" , "Amphibious creature" , "Went (anag.)" .)