In Egypt, many cases of granulomatous anterior uveitis consisting of single or multiple gelatinous nodules were detected in children living in rural areas. These lesions are believed to be waterborne and were previously attributed to flatworms ‘stage, showing some improvement after antiparasitic treatment. In a trial to explore the nature of these ocular lesions among rural Egyptian children, twenty surgically excised ocular lesions were subjected to transmission electron microscopy (TEM) examination. TEM results were combined with previous results of the metagenomic analysis performed for four cases out of the twenty samples, revealing the presence of Toxoplasma gondii (T. gondii), besides, a wide range of microbial communities, including variable species of fungi, bacteria, and archaea. The excised lesions ranged from 1 to 5 mm in size and demonstrated an extensive inflammatory cellular infiltrate. Using TEM, five out of twenty samples revealed active eukaryotic organisms with intact energetic cellular organelles, besides, numerous nuclei encircled within a syncytial layer and enclosed by a hyaline layer rich in mitochondria. Six samples showed inactivity in the cellular and the covering portions, while just inflammatory reaction was seen in the remaining nine samples. Toxoplasma gondii was found free within the distal part of the syncytium while, the proximal part showed the active synthesis of possibly extra polymeric substance, perhaps secreted by the microbial community. In a conclusion, Toxoplasma gondii has been detected among a microbial community in an atypical lesion in the eye. Further studies need to be sustained on genotype characterization, proteomic analysis, besides, the aquatic transmission of these mixed microbial species to the ocular tissues to clarify the reason behind such ocular illness.