The recent monsoon rains in Pakistan were unprecedented and caused flooding all over Pakistan, especially in Sindh and Balochistan. Following this national disaster, various water-borne and contagious diseases started erupting all over the country. In such a calamity-struck city of Jacobabad, we started receiving cases with a peculiar set of ocular complaints mimicking viral keratoconjunctivitis. Failure to respond to traditional treatment and the unique appearance of these corneal opacities led to a rare diagnosis of Microsporidial Keratoconjunctivitis, which was later confirmed by microscopy and staining of corneal scrapings of the most affected case. In line with published literature, all cases were treated with topical fluoroquinolone and topical anti-fungal therapy, following which the disease was cleared within a week. The disease has seen an upward trend the world over, especially among Asia. To the best of our knowledge, no such cases have been reported in Pakistan as yet. In this case series, we highlight the strong correlation of emergence of microsporidial keratitis in patients following exposure to pooled water bodies after the monsoon rainy season and floods. Moreover, this report will help create awareness in eye professionals regarding the prevention, timely diagnosis and treatment of these rare and emerging cases. Key Words: Keratitis, Spores, Water-borne diseases, Microsporidia.