A previously observed shift in the relationship between Chesapeake Bay hypoxia and nitrogen loading has pressing implications on the efficacy of nutrient management. Detailed temporal analyses of long-term hypoxia, nitrogen loads, and stratification were conducted to reveal different within-summer trends and understand more clearly the relative role of physical conditions. Evaluation of a 60-year record of hypoxic volumes demonstrated significant increases in early summer hypoxia, but a slight decrease in late summer hypoxia. The early summer hypoxia trend is related to an increase in Bay stratification strength during June from 1985 to 2009, while the late summer hypoxia trend matches the recently decreasing nitrogen loads. Additional results show how the duration of summertime hypoxia is significantly related to nitrogen loading, and how large-scale climatic forces may be responsible for the early summer increases. Thus, despite intra-summer differences in primary controls on hypoxia, continuing nutrient reduction remains critically important for achieving improvements in Bay water quality.