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Simple Summary: Evaluation of the respiratory system is a critical aspect of sea turtle medicine due to their peculiar anatomy. The location of the lungs under the carapace makes them vulnerable to wounds involving the carapace, which are frequent and significant complications of vessel strike injuries. Open lung wounds result in aspiration, loss of buoyancy control, and secondary infection. In sea turtles, pulmonary diseases can originate from many causes. Increased marine pollution is reflected in the increasing occurrence of sea turtles with entanglement injuries around the neck or flippers, caused by plastic waste, ghost nets, fishing lines, etc. These injuries may directly damage the upper airway or create life-threatening secondary infections. The object of the study was to describe clinical signs, radiographic, endoscopic and computed tomography examinations, and cytological and microbiological findings useful to obtaining an accurate diagnosis of pulmonary diseases in sea turtles. Moreover, we describe the treatment carried out on the basis of antimicrobial susceptibility testing to avoid unnecessary treatments and antibiotic-resistance phenomenon. Data were collected from 14 turtles. Radiographic signs of pulmonary pathology were seen in all cases. Four sea turtles underwent advanced diagnostic investigations so as to better characterize the pulmonary pattern. The bronchoalveolar lavage allowed us to withdraw fluid from the lower airways and to perform cytological and bacteriological examinations on all 14 subjects. The study suggests how it may be useful to implement diagnostic procedures in order to obtain an accurate and early diagnosis, to prevent unnecessary therapy, and to contain antibiotic-resistance phenomena. The aim of this study was to describe the clinical signs, radiographic, endoscopic and CT findings, cytological and microbiological findings and treatments of pulmonary diseases in sea turtles, in order to obtain an accurate diagnosis that avoids unnecessary therapy and antibiotic-resistance phenomena. In total, 14 loggerheads (Caretta caretta), with clinical and/or radiographic findings of pulmonary pathology, were assessed through various combinations of clinical, radiological, CT, endoscopic examination and bronchoalveolar lavage, which recovered fluid for cytologic and microbiologic analysis. In all cases, radiographic examination led to a diagnosis of pulmonary disorders—4 unilateral and 10 bilateral. All bacteria cultured were identified as Gram-negative. Antibiotic resistance was greater than 70% for all beta-lactams tested. In addition, all bacterial strains were 100% resistant to colistin sulfate and tetracycline. Specific antibiotic therapies were formulated for seven sea turtles using Enrofloxacin, and for four sea turtles using ceftazidime. In two turtles, antibiotic therapy was not included due to the presence of antibiotic resistance against all the antibiotics evaluated. In both cases, the coupage technique and environmental management allowed the resolution of the lung disease without antibiotics. All 14 sea turtles were released back into the sea. Radiographic examination must be considered the gold standard for screening sea turtles that show respiratory signs or abnormal buoyancy. Susceptibility testing with antimicrobials allowed appropriate therapy, including the reduction of antibiotic-resistance. [ABSTRACT FROM AUTHOR]