The black skimmer (Rynchops niger) is a state-threatened, colonially nesting seabird in Florida, USA. Conservation threats include habitat alteration, human disturbances, severe weather, and predation. During nest monitoring (May–September, 2020–2022), black skimmer juveniles at colonies on Fort Myers Beach and Marco Island, Florida, had polyarthritis and died or were euthanized due to severe illness. Similarly-aged skimmers from geographically distant (considered unaffected) colonies were evaluated for comparison (2021–2023). We documented field, clinical, radiographical, and pathological findings to characterize disease and purported pathogenesis. The majority were lame and lethargic, in poor nutritional condition, and dehydrated. Additionally, 8/23 of the skimmers with dermatitis and arthritis from affected colonies also had penetrating sandspurs associated with skin ulceration, scabbing, and/or hemorrhage. The affected joints were often in limbs (interphalangeal and hock; less commonly stifle, elbow, carpus). A postmortem evaluation and bacteriology revealed Staphylococcal aureus-associated dermatitis, arthritis, tenosynovitis, and/or osteomyelitis in 21/22 of the juvenile skimmers from southwestern nest colonies. Staphylococcus aureus dissemination to internal organs occurred in 10/13 of the skimmers tested. Among skimmers evaluated from distant colonies, 5/10 that were examined histologically had skin crusting and inflammation but lacked arthritis. Occasional coinfections were documented (e.g., West Nile virus, Gram-negative bacilli). The results suggest that staphylococcal joint disease originated from sandspur-induced skin damage, followed by hematogenous dissemination to the joints and, occasionally, the internal organs. Additional nest sites should be tested to evaluate disease risk and potentially contributing environmental factors. We recommend that site managers employ techniques that reduce the risk of skimmer interactions with sandspurs.