Are you sure the problem is with zebra mussels, and not some other type of mussel? Zebra mussels, such as those now found in the Great Lakes, cannot tolerate the ocean salinity level, thus, those that have washed down the Susquehanna River to Chesapeake Bay have never survived. However, there are some other forms of mussels that are similar in nature that tolerate higher salinity.
The bigger problem with any of this is the remedy is often far worse, environmentally, than the problem. For example, in the Chesapeake's upper reaches the power plant at Carroll Island once had a huge problem with entrainment of aquatic vegetation, sea worms, crabs and finfish, creatures sucked into their heat exchanger. The area in front of the plant, mainly the channel leading to the intakes, was treated with copper sulfate during the mid 1960s to kill off the grass, which also eliminated the habitat for the worms, crabs, finfish, etc... It worked. Every blade of grass from that area quickly died. Additionally, the massive volume of water pumped through the power plant circulated into the nearby waters of the Seneca River, Gunpowder River, Dundee Creek, Saltpeter Creek, and other smaller bay tributaries. The grasses died there as well. It took nearly 40 years for the grass to make a minor comeback in these areas, and some areas near the power plant have never experienced a resurgence. And, the more fragile, native species of aquatic vegetation, wild celery and eel grass, have never returned.
The smarter thing in this instance would have been to locate the power plant inland a few miles, a location where some of the water flowing down the Gunpowder River could have easily been diverted through the power plant's heat exchangers. At the time, the plant was a coal-fired facility that had the coal transported by rail to the facility. Later, when the plant converted to oil, it was transported to the facility by barge. The oil could have been transported from the Baltimore terminal by pipeline just as easily and at far lower cost.
Maybe I'm missing something, but I've never really understood the mentality of locating a power-plant along the shores of a bay or ocean, especially in an area where there are dozens of fast flowing rivers nearby that could do a far more efficient job.