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A mother and female calf humpback whale (Megaptera novaeangliae) pair were observed at an atypical location, 72 nmi inland in the Port of Sacramento, California, on 16 May 2007. Sequencing of mtDNA from a skin biopsy showed the cow to be an E1 haplotype, which is common in the California feeding population. Both animals had lacerations, suggesting sharp trauma from a boat strike. Photographs taken over 11 d showed generalized deterioration of skin condition and necrotic wound edges. Behavioral responses were recorded during attempts to move the animals downriver to the Pacific Ocean. The attempts included playback of alarm tones, humpback and killer whale sounds, banging hollow steel pipes ("Oikami pipes"), spraying water from fire hoses on the water surface, and utilizing tug and power boat engine noise and movement. None of these deterrents resulted in significant, consistent downstream movement by the whales. Antibiotic therapy (ceftiofur) was administered by a dart, representing the first reported antibiotic treatment of free-ranging live whales. After 11 d, the animals swam downstream from fresh water at Rio Vista to brackish water, and their skin condition noticeably improved 24 h later. The animals followed the deep-water channel through the Sacramento Delta and San Francisco Bay, reaching the ocean at least 20 d after first entering the Sacramento River.