Bay muds originate from two generalized sources.  First alluvial deposits of clays, silts and sand occur from streams tributary to a given bay.  The extent of these unconsolidated interglacial deposits typically ranges throughout a given bay to the extent of the historical perimeter marshlands.  Second, in periods of high glaciation, deposits of silts, sands and organic plus inorganic detritus (e.g. decomposition of estuarine diatoms) may form a separate distinct layer.  Thus bay muds are important time records of glacial activity and streamflow throughout the Quaternary period.
Some depositional formation is quite recent, such as in the case of Florida Bay, where much of the bay mud has accumulated since 2000 BCE, and consists of primarily decayed organic material.  In the case of Florida Bay these bay muds can accrete as much as 0.5 to 2.0 centimeters per annum, although the dynamic equilibrium of erosion, wave action redistribution and deposition complicate the net rate of layer growth. In the case of the Bristol Channel in the United Kingdom bay, mud formation has been occurring at least since the Eemian Stage (known as the Sangamonian Stage in North America), or about 130,000 years ago.  In other cases such as with San Francisco Bay, deposition has been interrupted by sea-level changes, and strata of vastly different vintages are found. In the San Francisco Bay Area, these are called Young bay mud and Older bay mud by geologists. Human activities can also affect deposition; close to half of the Young Bay Mud in San Francisco Bay was placed in the period 1855–1865, as a result of placer mining in the Sierra Nevada foothills.