Live and dead copepod abundances and environmental conditions were measured during summer in Chesapeake Bay to determine how population size, vertical position and non-predatory mortality varied with hypoxia. Abundances of copepod nauplii and Acartia tonsa copepodites decreased when low-oxygen water was present. Possible explanations include copepods altering their vertical position to avoid hypoxia, resulting in increased predation and advection losses. Alternatively, copepods residing in hypoxic water may experience increased mortality and sub-lethal effects of hypoxia on growth and reproduction. The vertical position of copepod nauplii did not appear to respond to hypoxia, but the vertical position of A. tonsa copepodites shifted upward in response to lethal hypoxia in bottom water. Non-predatory mortality of nauplii increased with the severity of hypoxia, but no similar increase was apparent for copepodites. Overall, it appears that hypoxia in Chesapeake Bay can result in lower copepod population abundances. Under moderate hypoxia, sub-lethal effects of low oxygen on growth and reproduction likely contribute to lower abundances, since the copepods do not avoid the hypoxic water. Under severe hypoxia, non-predatory mortality due to low oxygen is likely more important for naupliar stages, and the effects of altered vertical position on predation and advection may be important for copepodites.