A thousand fish in bottom of boat (4)
I believe the answer is:
keel
'bottom of boat' is the definition.
(I've seen this before)
'a thousand fish' is the wordplay.
'a thousand' becomes 'K' ('K' can be a synonym of 'thousand').
'fish' becomes 'eel' (eel is a kind of fish).
'k'+'eel'='KEEL'
'in' acts as a link.
(Other definitions for keel that I've seen before include "Low part of ship" , "Strut along base of ship" , "Longitudinal structure supporting the frame of a vessel" , "Cool, or it used to be" , "Vessel stabiliser" .)