Heavy units and siege should get a movement speed debuff when they are going through shallow water and stealth forests.
Crossing the water should be a difficult event for an army than walking on the ground. This will demand the player to consider water crossings when moving the army and add a bit of a barrier, in maps like canal.
Additionally You can add muddy ground mechanics to the game where some maps can have wet and muddy terrain which will require fighting with light units. This will emerge new playstyles for each civ in shallow water or muddy maps just like civs are played differently in water maps.