Many, but not all, fish kills in the summer result from low concentrations of dissolved oxygen in the water. Fish, like all other complex life forms, need oxygen to survive. They get theirs in the form of oxygen gas dissolved in the water. That's why it's important to have an aeration device, a bubbler, in your home aquarium. Warm water holds less dissolved oxygen than cold water, so summer is the time when fish can have a hard time getting enough oxygen. Other organisms use oxygen, too, including the algae that grow in the summer and bacteria that degrade organic matter. During the day, the algae produce oxygen through photosynthesis, but at night, when photosynthesis stops, they and other organisms keep respiring, using up oxygen. So on warm summer nights during algal blooms, the dissolved-oxygen concentration sometimes drops too low for the fish, and a die-off can occur. This can occur as a result of purely natural conditions or because of human activity that results in adding nutrients, nitrogen and phosphorus, to water systems. Nutrients come from many sources, fertilizers, automobiles, sewage, manure, and others. An excess of nutrients tends to speed up the growth of algae and diminish the availability of dissolved oxygen, especially in hot weather, sometimes resulting in fish kills. Low dissolved oxygen can result from other factors, too, such as poor flushing or circulation, dredging, or a sudden rain after a dry spell.
Fish kills also can occur as a result to toxic compounds released into a body of water. In order for this to occur, the toxic compound must be fairly highly concentrated. In a large water body (such as the Chesapeake Bay) this would require a very large amount of the toxic compound, and a release site fairly close to the affected fish.
Another cause of fish kills, which has had a lot of publicity in the last few years, is infections caused by fish pathogens such as the dinoflagellate, pfiesteria. If you would like more information about this topic, one source of information is the Web page USGS Chesapeake Bay Activities.