Wild birds are increasingly recognized as contributors to the circulation and environmental dissemination of zoonotic pathogens, yet data from Greece remain limited, particularly for raptors, corvids, and water birds. This study investigated selected parasitic, mycotic, and bacterial pathogens of public health relevance in free-living wild birds originating from various regions of Greece and admitted to two animal health care facilities. Between November 2023 and May 2025, cloacal swabs from 212 injured or sick birds were analyzed using quantitative PCR for Cryptococcus spp., Chlamydia psittaci, Giardia duodenalis, Cryptosporidium spp., and Mycobacterium avium. At least one pathogen was detected in 37 samples (17.5%), with Cryptococcus spp. being the most frequent agent (11.8%), followed by C. psittaci (3.8%), G. duodenalis (0.9%), and Cryptosporidium spp. (0.9%). M. avium was not detected. Pathogen occurrence varied by bird category, genus, and region, and was associated with health status. To the best of our knowledge, this study provides the first molecular evidence worldwide of G. duodenalis in Ardea spp., Cryptosporidium spp. in Asio otus, and C. psittaci in Botaurus stellaris and Plegadis falcinellus. These findings highlight wild birds as potential zoonotic reservoirs and support the implementation of One Health–oriented surveillance programs.