The most common among the snakes in Škocjanski zatok is Dice Snake (Natrix tessellata), which is the most numerous in Rižana left discharging channel and in the ditches in the freshwater part of the reserve, where they frequently feed on marsh birds broods. Less common is its nearest relative Grass Snake (Natrix natrix), also known as Water Snake or Ringed Snake. Drier shruby areas host a very fast Western Whip Snake (Coluber viridiflavus).
The nature reserve is also a home to European Pond Turtle also known as European Pond Terrapin (Emys orbicularis), which is hard to detect due to its secretive way of life.
Walking along the circular trail the reserve’s most common Italian Wall Lizard (Podarcis sicula campestris) can easily be observed. It is found anywhere in the open areas with the greatest numbers along the embankment between Bertoška bonifika and brackish lagoon.