Much of the Bay is shallow. At the point where the Susquehanna River flows into the Bay, the average depth is , although this soon diminishes to an average of  southeast of the city of Havre de Grace, Maryland, to about  just north of Annapolis. On average, the depth of the Bay is , including tributaries; over 24 percent of the Bay is less than  deep.
Because the Bay is an estuary, it has fresh water, salt water and brackish water. Brackish water has three salinity zones: oligohaline, mesohaline, and polyhaline. The freshwater zone runs from the mouth of the Susquehanna River to north Baltimore. The oligohaline zone has very little salt. Salinity varies from 0.5 ppt (parts per thousand) to 10 ppt, and freshwater species can survive there. The north end of the oligohaline zone is north Baltimore and the south end is the Chesapeake Bay Bridge. The mesohaline zone has a medium amount of salt and runs from the Bay Bridge to the mouth of the Rappahannock River. Salinity there ranges from 1.07% to 1.8%. The polyhaline zone is the saltiest zone, and some of the water can be as salty as sea water. It runs from the mouth of the Rappahannock River to the mouth of the Bay. The salinity ranges from 1.87% to 3.6%. (3.6% is as salty as the ocean.)
The climate of the area surrounding the Bay is primarily humid subtropical, with hot, very humid summers and cold to mild winters. Only the area around the mouth of the Susquehanna River is continental in nature, and the mouth of the Susquehanna River and the Susquehanna flats often freeze in winter. It is rare for the surface of the Bay to freeze in winter, something that happened most recently in the winter of 1976–77.
The Chesapeake Bay is the end point of over 150 rivers and streams. The largest rivers flowing directly into the Bay, in order of discharge,  are:
* Susquehanna River
* Potomac River
* James River
* Rappahannock River
* York River
* Patuxent River
* Choptank River
For more information on Chesapeake Bay rivers, see the List of Chesapeake Bay rivers.