The physico-chemical properties of the lower reaches of the Cross River estuary were studied in the wet season month of September, 2011. A total of 50 bottom water samples were obtained using a Nansen Bottom Water Sampler, at 50 geo-referenced stations within the channel. Depth measurements were simultaneously taken at each station using an echo-sounder, while turbidity was measured using a secchi-disc. Temperature, salinity and pH were analysed for each sample, using a HANNA hand held combo meter (HI 98129). Within the channel, bottom water temperature ranged between 23 and 30°C, turbidity (transparency) ranged between 30 and 100 cm, pH ranged between 5 and 9, while bottom water salinity ranged between 0.15 and 0.20 ‰. Based on salinity, the channel was divided into 3 physico-chemical facies: the Upper Facies is fairly saline, characterized by temperatures ranging from 25 to 26°C, is the least turbid segment of the channel and isalkaline the Middle Facies, the least saline part of the channel, characterized by temperatures ranging from 24 to 29°C, most turbid, and neutral,; and the Lower Facies, the most saline portion of the channel, with temperatures ranging from 25 to 29°C, is the more, acidic, part of the channel. The estuary appeared to have been greatly diluted. This may be attributed to the fact that the study was carried out during the rainy season. As a result of the high freshwater discharge into the channel during this season, the freshwater-brackishwater interface has been driven further downstream, towards the Atlantic Ocean