I live on a shallow and weedy end of Hayden Lake; between that and hunting I have seen and dealt with a lot of milfoil.
On Hayden, a combination of techniques are used to combat milfoil. In lightly infested areas, diver pulling is used. Milfoil cannot be mechanically harvested, because the smallest fragment (and I mean tiny) can start a new plant. Diver pulling is practical in areas with steep shorelines, since milfoil only grows to a certain depth and infestation is light. Divers gently pull the plant out roots and all, then vacuum it up to a surface boat via a hose and pump arrangement.
The shallow areas, where milfoil can grow into a thick, choking mat is where herbicide treatment is really the only alternative. As far as Hayden Lake is concerned, the EPA has limited spraying to 85 acres over the last five or six years. There are hundreds of acres thickly infested. Therefore every bad area gets a kiss and a promise every few years...the herbicide works well...while fragments increase the milfoil density in other areas of the lake exponentially. Boat props are the main culprit in the dicing up of milfoil strands and they do a very efficient job. This provides the possibility for every single plant to spawn hundreds of new plants.
The herbicides used are as far as I know specific for certain plant types and do not kill off all the plants in the lake. Nor have I ever seen a fish kill, a dead bird or any other indication that wildlife is harmed. Overall I think it is very safe.
I can tell you with absolute certainty that the milfoil problem on the Pend Oreille River is getting much worse. Downstream in Washington it is critical. At this point, herbicide seems to be the only answer. The state of Idaho has recognized this and has budgeted millions of dollars for spraying and diver pulling. The battle has been stepped up on Hayden Lake and we had spraying of a much larger lake area last week. It's business as usual over the 4th of July.