Agnes was barely a hurricane at landfall in Florida, and the effects of winds and storm surges were relatively minor. The major impact was over the northeastern United States, where Agnes combined with the non-tropical low to produce widespread rains of 6 to 12 inches with local amounts of 14 to 19 inches. These rains produced widespread severe flooding from Virginia northward to New York, with other flooding occurring over the western portions of the Carolinas.

The worst flooding was along the Genesee River, the Canisteo River, and the Chemung Rivers in southwestern and southcentral New York. The latter two flow into the Susquehanna River and flooding continued all the way down this river. The worst damage occurred in Elmira, New York and Wilkes-Barre, Pennsylvania, but many other communities along the rivers suffered great losses. So much fresh water was flushed into Chesapeake Bay that its seafood industry was badly damaged for several years.

Agnes caused 122 deaths in the United States. Nine of these were in Florida (mainly from severe thunderstorms) while the remainder were associated with the flooding. The storm was responsible for $2.1 billion in damage in the United States, the vast majority of which came from the flooding. Agnes also affected western Cuba, where seven additional deaths occurred.