I'd do a hallow or an unhallow, maybe with a unique effect or two linked.
Baleful Polymorph: tadpole
Dispel Magic
Rusting Grasp on one item per character
Silence
Dimensional Anchor
or maybe have pit be full of weak acid, and it casts a constant resist energy on the crocodiles. (The acid would need to be weak enough that it'd never break through the resistance; if it is cast by an 11th-level caster, for example, the acid should inflict no more than 5d6 points of damage/round to submerged creatures).
Alternatively, use wight crocodiles, and have the water infused with negative energy, inflicting 5 points of negative energy damage/round to the living and 5 points of healing to the undead.
Daniel