Deep water shelter put up around small port (6)
I believe the answer is:
depths
'deep water' is the definition.
(I've seen this before)
'shelter put up around small port' is the wordplay.
'shelter' becomes 'shed' (I've seen this in another clue).
'put up' says the letters should be written in reverse.
'around' means one lot of letters goes inside another.
'small port' becomes 'pt' (abbreviation; 'small' indicates an abbreviation).
'shed' reversed gives 'dehs'.
'dehs' enclosing 'pt' is 'DEPTHS'.
(Other definitions for depths that I've seen before include "Lowest levels" , "Distances down or front to back" , "Sea bottom" , "Demoralisation" , "Extents downward, backward or inward" .)