With the advent of the Acquired Immune Deficiency Syndrome (AIDS), the human host has become susceptible to most opportunistic pathogens. Some of these organisms are the emerging protozoan entero-parasites; Cryptosporidium spp and Giardia spp. The aim of this study was to isolate and identify the oocysts of Cryptosporidium spp and cysts of Giardia spp in the surface water of Yaoundé, Cameroon, using the standard(UnitedStates Environment and Protection Agency) USEPA Method 1623, which is based on ultrafiltration, immuno-magnetic seperation and fluorescence antibody. The analysis lead to the determination of some ecological factors of the aquatic ecosystem, which are turbidity, suspended solids , ammonia, Biochemical Oxygen Demand and the correlation between the biodynamics of the (oo) cysts in the medium characterised. These particles could play an important role in the transportation of the (oo) cysts in the aquatic medium by an adsorption mechanism. Our results obtained for the surface water suggested an increase in the pathogen densities from upstream to downstream. The minimum-maximum values recorded for the for Giardia cysts along the Mfoundi , were 7-15 cysts/L , 12-38 cysts /L and 31-98 cysts/L respectively. The minimum –maximum values recorded for the Cryptosporidium oocysts from upstream to downstream of the Mfoundi, were 4-6oocysts/ L, 18-54 oocysts / L and 26- 64 oocysts/ L respectively.