Organisms of the genera Cryptosporidium and Giardia are enteric parasites that are responsible for cryptosporidiosis and giardiasis respectively. They are characterised by profuse diarrhoea, abdominal pain and cramping. The symptoms can be fatal for immunodepressed subjects and children because these are opportunistic pathogens. These pathogenic infections are rampant in developing countries due to the unhygienic and improper disposal of wastewater and the use of surface water as the major sources of potable water. Little information is available about the resistant forms of these microorganisms in the hydrosystems of Cameroon in particular and other sub-Saharan ecosystems in general. The aim of this research was to isolate, identify, and measure these forms of these emerging protozoa in the waste and surface waters of Yaoundé, Cameroon. Giardia spp cysts were identified by Lugol iodine staining, and the Cryptosporidium spp oocysts by the Ziehl-Neelsen technique. The cysts were oval in structure and varied in length from 7 um to 12.0 um. Axostyles were visible along the median line and nuclei were present. The oocysts were round in structure and varied in diameter from 4 um to 6 um. A double cell wall was seen in the apicomplexa. The highest concentrations of Giardia spp cysts were 560 cysts/L in the surface water and 650 cysts/L in the residual effluent, while the corresponding figures for Cryptosporidium spp were 1,110 oocysts/L in the stream and 1,500 oocysts/L in the effluent. The cyst and oocyst counts were higher in the direct effluent because they are released directly into the wastewater by feces, while they are diluted in the surface water, reducing their abundance. Turbidity has a significant effect (p<0.05) on the population dynamics of these microorganisms, thereby indicating the importance of suspended or colloidal particles in the dissemination of these pathogens in aquatic media. The suspended particles in the wastewater adsorb the oocysts and cysts, probably because of the interactions between the electric charges carried by suspended particles and those present at the surface of the parasites. The positive correlation observed between these parasites and ammonia may account for some of the die-off of these resistant forms, because ammonium ions in water are known to inactivate trophozoites and sporozoites present in cysts and oocysts. This may be due to the permeability of the protozoan membrane to the ammonium ion and other alkaline earth metals present in aqueous form in the biotope. These parasite forms in these media represent a considerable health risk to the inhabitants of the study zone who depend on this surface water for drinking. The small size of these parasitic forms, the nonfunctional water purification stations and ineffective water treatment systems expose the community to outbreaks of giardiasis and cryptosporidiosis.