Back in 2003, Alex Alvarez of Gnomon had a FREE video tutorial on this EXACT subject called:
"Water Flow using Parametrization in Maya"
Alex long-since removed it due to the technique being depreciated and replaced with newer features in the "Surface Flow" feature.
I have the video on my server so PM me and I'll get you the link to download it if you want
You can also try checking the help for texture emission attributes, and try controlling rgb surface texture emission particle flow with well placed/animated fields:
*Use a texture to color emission or scale the rate:
User Guide > Dynamics and Effects > Dynamics > Particles > Work with emitters > Use a texture to color emission or scale the rate
Come to think of it, if a simple flow is all you need, why not just try using the particle flow node along a path on your surface?
Israel "Izzy" Long
Motion and Title Design for Broadcast-Film-DS