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Assessment of water chemistry in a segment of Qua Iboe River Estuary, Niger Delta Region of Nigeria was carried out from January to December 2018 at three sampling stations. Seventeen physico-chemical parameters were analyzed using standards procedure. A total of 12 samples were collected from each station. Principal Component Analysis (PCA) was employed in the assessment of the study area. Three principal components, accounting for 99.59%, 100.01% and 100% of the total variance of information contained in the original data set for dry season were obtained. In the wet season, the components accounted for 66.0%, 69.97% and 67.50% of the total variance respectively. Results revealed that the most loading factor in the PCA when considering all the sampling stations in different seasons together in PC1, PC2 and PC3 axes were mainly sulphate, phosphate-phosphorus, calcium, potassium, temperature, total dissolved solids, total alkalinity, total hardness, dissolved oxygen, sodium, electrical conductivity, biological oxygen demand, pH, total suspended solids, A and magnesium. These loadings could be grouped into mineral/nutrient, physico-chemical, organic and domestic factors. General assessment of the study area did not indicate much deviation from prescribed standards, but sufficient to maintain a varied aquatic biodiversity.