I use NetLogo quite a lot. In that platform, you can create exchanges with the landscape (patches, representing the two-dimensional space of your world) and agents (mobile elements, that can represent farmers or industry, etc.)
You can specify some patches in your "world" as water resources of different types. See the El Farol model in the Netlogo Models Library (that come with Netlogo).
For your domain, consider the WaterScape model by Erin Bohensky, available in the OpenABM library.
For a much more detailed example of a Netlogo model that incorporates historical data, geography, water resources, and human interaction over time, see the wonderful work of Scott Heckbert with his MayaSim model, also available in the OpenABM library.