EcoFluxx is like its parent game Fluxx, only a lot more complicated; there are a few new types of New Rule ("Composting" gives you the option of drawing from the discard pile instead of the draw pile, and the "Inflation" cards increase all numbers on all cards).
The other major change (also used to a limited degree in Zombie Fluxx) is that, whilst two keepers are still needed to meet a Goal, they are no longer required to be controlled by the same person. Most of the Goals involve parts of the food chain, to fit in with the game's ecological theme; an example is "Bears eat Fish"- the person with Bears in front of them win if Fish is also on the table.
Further, Creeper cards prevent everyone from winning, rather than the player holding them, and cards like "Poison" (which makes all a player's animals poisonous) further enforce the idea that everyone needs to pay attention to the state of the board.
There's also an 'Extinction' card that takes one Keeper (species) out of the game. Not just out of play for the moment, but back in the box until the next game. Depressing but appropriate.
Games take longer than regular Fluxx and it's a more thinky game.