Background and Aim Sperm morphometry is a vital indicator of fertility, yet male germ cells are highly vulnerable to environmental toxins such as heavy metals. Dromedary camels (DCs) are frequently exposed to penile and preputial pathologies, conditions that can impair semen quality. This study aimed to assess epididymal sperm morphometric characteristics in camels with genital lesions and to explore their associations with concentrations of aluminum (Al), zinc (Zn), molybdenum (Mo), nickel (Ni), and lead (Pb). Materials and Methods Sixty adult male DCs (8–10 years, n = 10/group) were classified into six groups: injury-free, balanoposthitis, penile trauma, prolapsed prepuce, phimosis, and penile tumors. Blood samples were analyzed for heavy metal concentrations using inductively coupled plasma mass spectrometry. Epididymal spermatozoa (caput, corpus, cauda) were evaluated for sperm length (SL), sperm head length (SHL), sperm head width (SHW), sperm head length-to-width ratio (SHL/W), and sperm tail length. Sperm abnormalities were categorized into proximal/distal cytoplasmic droplets and tail defects. Data were analyzed by analysis of variance and correlation statistics. Results Sperm morphometrics varied significantly with pathological status. Camels with penile and preputial disorders exhibited increased SHW in caudal spermatozoa, while SHL and SHW were reduced in caput spermatozoa (p < 0.01). The phimosis group showed fewer abnormalities and lower total abnormal sperm, whereas the penile tumor group had elevated proximal and distal defects and the highest abnormality rate. Heavy metal analysis revealed significantly increased Zn and Ni concentrations in the penile tumor group, while Mo and Pb levels showed no significant differences. Correlation analysis indicated strong associations of Al and Zn with SHW and SHL/W in caudal spermatozoa, and Ni with SHL, SHW, and SHL/W in corpus spermatozoa (p < 0.05). Conclusion Epididymal sperm morphometrics are influenced by penile and preputial pathologies and are significantly associated with Al, Zn, and Ni concentrations. These findings highlight the potential role of heavy metal accumulation in camel reproductive dysfunction and emphasize the need for monitoring environmental exposure in breeding regions.