This study investigated the pathogenic bacteria diversity in African catfish (Clarias gariepinus), their seasonal variations, and public health significance. 135 samples were collected from the skin, gill and guts of 45 adult catfish from three major fish farms in Ota. Microbiological analysis was conducted on them during rainy, harmattan and dry seasons between April 2019 and February 2020 to determine the bacterial load and identify various pathogenic bacteria. Data collected were analyzed using Analysis of Variance. High bacteria diversity was observed across the three seasons and study areas. The total aerobic count of the gut at Royal Fish Farm (1.24×107±0.06c) was significantly higher (P˂0.05) than that from the gill (7.88×106±1.22b), while at the gill, it was also higher than found in the skin (6.08×105±0.18a) during the rainy season. The same trend was observed during harmattan season (1.93×107± 0.28c, 1.45x106 ±0.06b, 8.44x105 ± 0.92a) and dry season (2.14x108 ± 0.03c, 1.56x107 ± 0.07b, 1. 45 x106 ± 0.03a). A similar trend was also observed at Farm 360 and Oluwadare Farm. Given the high contamination of bacteria pathogens recorded in this study, which exceeded the recommended limit of ˂5.0x105 colony forming unit by the International Commission for Microbiological Specification for Food, these fish can pose a high risk to human health if consumed. Given this, It is hereby recommended that the government should strictly enforce the environmental protection law to prevent indiscriminate disposal of industrial effluents and to keep the water body safe for aquatic lives and agricultural use.