An interesting idea for a Earth/Water synergy would be to make an Earth card that aided Field cards in some manner. Such as for flooding, a new Earth card akin to "Climate Shift: Amplify and enhance the effects of Field cards."
For flooding I'm not sure what it could do, perhaps it could make the last 5 areas of the field 'shallow' water, whereby being all non-water non-nautral creatures
Of course the flip side would to make this not a forced combination. Which would be as simple as adding several other field cards in the same vein as Flooding, and then adding a climate shift to them.
Perhaps something for Air like "Tempest: Deal 1 damage to all non-air creatures on the field each turn." Or for Fire, like "Volcanic Turf: Whenever a Fire card is played, deal 2 spell damage to a random creature/player." Perhaps it could even work for Nightfall/Eclipse as well.
I might flesh out a couple cards in full depicting this kind of synergy, if I feel sufficient inspiration. But the general idea would give earth and water a synergy