TL;DR: Water is finite. Making power takes cold water and produces hot waste water. Biters live in the lakes and draining the lakes or dumping hot water back into them pisses them off.
1. Water as a finite resource
Lakes now have capacity, dependent on their area. Drawing water from them via pumps draws from this capacity. Water naturally regenerates at a rate proportional to the maximum. When the water level drops, the lake shrinks visually (it starts turning brown from the edges towards the center). The lower the water level, the faster the regeneration, so that for any given rate of drain the lake will reach an equillibrium. If the lake is emptied water cannot be drawn faster than the maximum rate of regeneration.
Bonus idea: lakes in deserts regenerate much slower.
Question: but if the water recedes from the shore, how will offshore pumps keep working?
Answer: make the offshore pump spawn a small pipe that goes to the deepest part of the lake, so it's always connected.
2. More use for water
Water being limited only matters if you have a use for a lot of it.
Idea: Make power generation require lots of water.
Boilers now produce "steam". It still behaves like a liquid, because it really doesn't matter.
Steam engines have two inputs and one output. They take steam and cooling water and output hot water. The colder the cooling water, the more power they produce. The hot water needs to be dumped.
Having a large power plant now means you need to draw lots of cold water and find a place for lots of hot water. Adds another dimension to power production, which I think is far too simple right now.
3. Heat pollution
We have hot water and we need to do something with it.
Hot water can be simply dumped back into a lake. This causes heat pollution. It behaves exacly like the current pollution, but spreads through water. A water pump on a poluted lake will produce water warmer than the default 15 degrees, proportionally to the severity of pollution.
So you can:
- Dump the hot wastewater into the same lake as you took it from. You keep the water level high, but you heat it up, reducing the efficiency of your power plant.
- Dump it into the same lake, but pipe it further away. You reduce the power loss, but you need to make long and vulnerable piping. Why "vulnerable" - see section 4.
- Dump it into another lake. This will cause a drop in the water level of the first lake, but you lose no efficiency.
4. New enemies - more reasons to avoid draning water and pollution
There are aquatic biter nests in the water. The biters come out and attack when the dropping water level exposes their nest, or when they're hit by heat pollution. This is analogous to the already existing mechanic of pollution baiting biters. The deeper the nest, the stronger the biters, so that the more water you draw the more you have to deal with attacks.
To sum up: water is now a valuable, limited resource, there is an important use to it, and there's a challenge to obtaning it. I think it makes things a lot more interesting.
It doesn't change much in the early game - you only need a second pump and a bit more pipe; you won't be using enough water to create an issue. So no problem for newbies. But in the late game, it can have major consequences.
Bonus idea: this provides an opportunity to implement nuclear power in an interesting way. A nuclear reactor will probably be just a burner that runs on refined uranium, which is not very interesting, but let's make it require huge amounts of cooling water. This makes choosing a proper location for a nuclear power plant very important, and creates a significant drawback (you need lots of cooling towers or you'll have lots of pissed off biters). And it's even realistic.