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The study into the microbial quality of coconut water and its impact on the quality of the extracted coconut oil was carried out with the aim of determining microbial load of freshly harvested and marketed coconut fruits water and also assess the impact of the isolated fungi on the acid value and density of the coconut oil. Fungi associated with the different coconut samples was isolated using the pour plate techniques while the impact of fungi on the oil quality chemical was determined using the analytical method described in Association of Official Analytical Chemists (AOCS) manual. The results of the fungi associated with the different coconut water revealed the presence of fungi such as A. niger, A. fumigatus, A. tamari, A. flavus, Lasidiopodia, and Penicillium spp. Penicillium sp. was found to be more prevalent in all the samples with percentage occurrences of 49%, 60% and 72% in samples obtained from Olokun, Iguosa and New Benin markets respectively while Lasidiopodia sp. had the lowest percentage occurrence of 3% from the samples obtained from Iguosa market. Freshly harvested coconut water had no microbial growth. Aspergillus niger having the highest AV of 4.2% compared to Lasidiopodia which had 4.0% at day 15. The fungal isolates also ability to alter the density of the coconut oil when compared with the control. The findings from this study have shown that freshly harvested coconut water is free from fungal contamination when compared to marketed coconut water also the isolated fungi have the ability to cause deteriorative effect on the quality of the oil.