Relation between a compound's toxicity and it's concentration level
The article at linked at the bottom says that the marine organisms keep the concentration of Ammonia under very strict control. 


pH of the ECF (Extra Cellular Fluid) is said to play a very important role. 
The concentration of ammonia in the environment (ambient ammonia levels) also plays an important role. 
Less importantly temperature also plays a role.
Ionic strength of water also is involved.


The NH3:NH4+ ratio seems to be more important than the abosolute value of ammonia.



Ammonia is more toxic than ammonium ion. The lipophilic (ammonia is amphiphilic - soluble in both water and lipid) nature of ammonia allows it to easily cross the cell membrane and the blood brain barrier (in organisms where BBB exist) and affect the physiologic functions. The ammonium ion on the other hand can't enter the cell as easily, as it is not as soluble in lipid as ammonia.




For ammonia and marine organisms see http://www.sciencedirect.com/science/article/pii/S1546509801200053
For more on ammonium toxicity see: http://www.ucl.ac.uk/~ucbcdab/urea/amtox.htm