Biology/Natural History: This species lives in pairs in permanent, U- or Y-shaped burrows in mud flats, usually lower in the intertidal and in muddier areas than does Neotrypaea. The burrows usually have several entrances, and may connect horizontally to the burrow of nearby mud shrimp. For burrowing they carry mud in a "basket" formed by the first two pairs of thoracic legs. Once removed from the burrow as adults they do not seem to be able to dig another one. They feed on suspended detritus carried into their burrow by the beating of their pleopods and captured by their hairy first two pairs of thoracic legs. The fifth pair of legs is used both for walking (with legs 3-4) and for cleaning the body (plus the eggs of females). Many commensals such as the northern hooded shrimp Betaeus harrimani, the snapping shrimps Betaeus ensenadensis and B. longidactylus, Scleroplax granulata, the crab Scleroplax granulata, the pea crabs Pinnixia franciscana and P. schmitti, the scale worm Hesperonoe complanata, the clam Cryptomya californica, the phoronid Phoronis pallida, and the arrow goby Clevelandia ios live in the burrows. Upogebia also seems to have many parasites including an isopod which frequently lives in the gill chambers of specimens from Padilla Bay, the clam Pseudopythina (formerly Orobitella) rugifera which lives attached to the pleopods (picture), and the isopod Phyllodurus abdominalis, which also attaches to the pleopods. The copepod Clausidium vancouverense lives on the outside of the body. Upogebia lays yellow eggs in fall which do not hatch until spring. Predators include Pacific staghorn sculpin Leptocottus armatus. Mud shrimp disrupt commercial oyster beds and smother the oysters. This species can tolerate brackish water down to 10% of seawater salinity, by osmoregulation.

In a study in Oregon's Yaquina Bay where Upogebia pugettensis is very abundant, 57% of males and 80% of females were infested with the parasitic, blood-sucking bopyrid isopod Orthione griffinis (Smith et al., 2008) Infestation was especially prevalent among larger Upogebia and in females. Infested hosts were an average of 7.8% lower weight than similar-sized uninfested hosts. Burrowing by the species increased remineralization of carbon compounds in the sediment by up to 2.9 times, ammonification by up to 7 times, nitrification by 3 to 9 times, denitrification by up to 4 times, and up to a 15-fold increase in flux of dissolved inorganic nitrogen.