Do rivers cause eco-damage in Sid Meier's Alpha Centauri?

Although the internet has non-authoritative (opinion) answers to your question [see 'terraforming hints', here], the game user manual (starting at the 'ecological risks' section [on page 54]) reads as follows (my comments are in the [] brackets):

'...each technological enhancement constructed on any square in a base's production radius increases that base's ecological disruption. In general, the more complex an enhancement (i.e. the longer it takes to complete), the greater the damage it causes. Also, the higher a base's mineral production, the greater the chance of ecological disaster.'

'Your ecological damage ranking, as shown on your base screen [under the label 'eco damage'] gives a percentage chance on each turn that Planet will react to your disruptions in the form of uncontrolled fungus blooms that wipe out all existing enhancements in a given square, The new fungus also often spawns native life forms.'

'Ecological damage can be minimized (or even eliminated entirely) through social engineering ['green' is especially good for this] and secret projects (such as the Pholus Mutagen).'

So the although the user manual seems to imply that any change you make to a square [including drill to aquifer] will cause some ecological disruption, this is not always true. I have found that while building farms, mines, roads, and especially boreholes increases eco disruption, building forest or fungus in squares [non-technological terraforming] tends to decrease eco disruption and some terraforming, like 'drill to aquifer', or raise/lower/flatten terrain are more or less neutral to eco disruption.

In general, if you plant sufficient forest and fungus squares and don't have too high a mineral production in any given city, eco disruption is easily avoided, even if you do a lot of terraforming.