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Seasonal effects on microbial load of sediment and water at different locations along Bonny Estuary of Niger Delta was investigated for a period of 12 months. All analyses followed standard procedure. Results revealed that total fungi counts in sediment and water at different locations were not significantly different (p > 0.05) at both wet and dry seasons while hydrocarbon utilizing fungi showed significant differences (p < 0.05) at both seasons in both sediment and water samples. During the wet season, total faecal counts ranged from 5.0 to 10.0 x 105 CFU/g for sediment and 4.0 to 7.0x 105 CFU/g in water. In dry season, the concentration of hydrocarbon utilizing bacteria in the sediment ranged between 0.1 x 105 CFU/ml/g and 8.0 x 105 CFU/ml/g in wet season while in dry season, the concentration in water ranged between 0.1 x 105 CFU/ml/g and 6.0 x 105 CFU/ml/g at Abuloma. At Okwujagu, total heterotrophic bacteria counts in sediment ranged from 0.1 to 8.0 x 105 CFU/g in dry season. This was higher than the range 0.1 to 6.8.0 x 105 CFU/ recorded in Abuloma, Okwujagu and Slaughter at dry season. The highest vibrio counts in water (11.0 x 105 CFU/ml) for wet and (10.0 x 105 CFU/ml) for dry seasons were recorded at Slaughter. In Oginiba, the feacal count recorded 3.0 x 105 CFU/ml in water during the wet season and 2.0 x 105 CFU/ml for dry season. Generally, there were significant differences (p < 0.05) in the bacterial concentrations in both sediment and water. This showed that different seasons favour the growth of certain microbial types.