Throughout the winter season (October 2020–April 2021), there were substantial changes to the taxonomic composition, abundance, and diversity, especially in the sampling immediately preceding and during the sewage fungus incident (Figure 1). At the control site upstream of the surface water discharge, the community composition shifted over the sampling period, but there were no substantial changes in diversity (4.303–4.555) or evenness (0.675–0.721) (Table 1). Whilst the relative abundance of the taxa (represented as the lowest taxonomic unit) changed over time, no single taxa was dominant; for example, the greatest relative abundance of OTUs based on the lowest taxonomic unit was 7.1% (Figure 1(a)). The impact site had similar diversity, richness, and evenness to the control during early winter (Oct20 and Dec20). However, from Dec20 to Feb21, there was a reduction in the diversity by 42%, from 4.375 to 3.204, and the evenness also reduced by 38.7%, from 0.693 to 0.501 (Table 1). Diversity and evenness remained consistently low during the sewage fungus incident but increased to values comparable to the control in the Apr21 sampling suggesting a recovery of the periphyton community in terms of evenness and richness.