Waterborne Coccidians are emerging pathogens and are not entirely known in developing countries. Cryptosporidium and Cyclospora have been reported to cause diffuse watery diarrhea among immunocompetent and immunocompromised individuals alike but are not included in routine water quality examinations and medical diagnosis thereby leading to being underreported, undiagnosed or misdiagnosed and neglected as agents of intestinal-protozoan ailments. Water samples from a major watershed in Metro Manila, Philippines were investigated. A total of 99 samples (50-mL each), were filtered to obtain sediments that were processed and smeared onto glass slides and stained using modified Kinyoun’s acid-fast technique and microscopically observed for Cryptosporidium and Cyclospora oocysts. The 3-day collection (33 samples per day) returned positive results: Day 1 returned 42% (14/33) positive water samples, Day 2 with 85% (28/33) and Day 3 with 88% (29/33) for Cryptosporidium and Cyclospora oocysts. Overall, oocyst positivity was 72% (71/99). The results of this study support previous Coccidian findings in a major Philippine watershed and calls for further exploration of source water samples for intestinal protozoan pathogens, the identification of which can lead to initiatives in improving water quality assessment and the prevention of the transmission of waterborne protozoan pathogens to the general public.