Cryptosporidium is an apicomplexan parasite known to cause gastrointestinal disease in humans and several animal hosts including piscines. To determine the occurrence of Cryptosporidium in catfish, Clarias gariepinus, and their aquatic habitats from the wild and cultured environments, 400 catfish from two dams (n = 100) and six backyard catfish farms (n = 300) as well as 40 water samples of 20L each from the dams (n = 10) and 10L each (n= 30) from six backyard farms were examined in Zaria, Kaduna State, Nigeria. The fish gut contents were concentrated using formol-ether concentration technique, whilst the water samples were concentrated using sedimentation and centrifugation techniques. All processed samples were stained with modified Ziehl-Neelsen method and morphometric measurements of oocysts taken with the aid of a calibrated eyepiece graticule. One hundred questionnaires were also administered to catfish consumers within the study area, this was to obtain information on their level of awareness on diseases associated with catfish and their hygiene practices after handling catfish. Basic objectives of this study were to determine the followings; the prevalence of Cryptosporidium in catfish and its water habitat, the effect of the physico-chemical parameters of the water habitat of catfish on occurrence of Cryptosporidium in water sampled within study area, as well as the association between the prevalence of Cryptosporidium in Clarias gariepinus and management practices of catfish farmers in the study area. Cryptosporidium oocysts were found in 86 (21.5 %) out of the 400 fish, and 3 (7.5 %) out of the 40 water samples with oocysts of 3 different size ranges, corresponding to the following species; C. molnari –50.0 % (4.69 µm ± 0.07 × 4.46µm ± 0.29), C. parvum – 45.3 % (5.05µm ± 0.12 × 4.49 µm 0.04), and C. andersoni – 4.7 % (7.40µm ± 0.47 × 5.60 µm ± 0.49). Of the four physico-chemical parameters (temperature, pH, dissolved oxygen, and turbidity) measured, only turbidity was found to have a significant effect (P < 0.05) on the occurrence of Cryptosporidium in water sampled within the study area. Wild catfish were significantly more infected with Cryptosporidium oocysts than the cultured ones (OR = 1.962; 95% CI 1.204 < OR < 3.196; P = 0.0078). Cryptosporidium oocysts were higher (10.0%) in dams as compared to 6.7% in water from backyard farms. The prevalence of Cryptosporidium oocysts in the bigger catfish within 451 to 850g was 28.0% compared to 21.1% in the smaller ones that were within 150 to 450g. Similarly, the prevalence was slightly higher (22.2%) in the lengthier (36 – 55cm) catfish than in the smaller ones (21.1%) within 15 – 35cm in length. The prevalence was also higher in male catfish (24.4%) than in females (19.2%). Based on management practices of catfish farmers, frequency of pond water replacement (P = 0.0008) and method of dead fish disposal (P = 0.04) were significantly more commonly associated with the occurrence of Cryptosporidium in backyard farms, whereas, type of pond, source of water, frequency of cleaning ponds and prophylactic medication to fish were not significant (P > 0.05). A significant number of the catfish consumers were unaware of any disease associated with catfish consumption (70.0%) or the zoonotic risks of any disease of catfish (86.0%). The presence of Cryptosporidium oocysts in catfish and their water habitats in the study area is of public health concern indicating the possible health threats posed to consumers and handlers.