I feel your pain. I acutally work for MDC and have attempted to deal with situations like this in the past. It truely falls back on the developer and the DNR to enforce the clean water laws that have been inacted.
A couple of years ago I was dealing with a landowner that had a complete fish kill due to over application of poultry litter and couldn't get any responce either. Extremely frustrating to have that kind of investment destroyed with no easy way to be compensated.
I do know that about 10 years ago the biologist on the Reed Area (Lees Summit) was able to receive compensation for the devlopment that went in within the watershed so there is a legal precedent.