Human activities in lake catchments and waterways have a considerable detrimental impact on lake ecosystems, including processes such as eutrophication and siltation. The study’s objective was to gain a deeper understanding of the impact of anthropogenic activities on water quality, pollutant diffusion in Lake Batur waters, and the level of eutrophication. Water samples from nine sampling locations (SLs) in Lake Batur, Indonesia, were collected and examined for physical, chemical, and biological properties. The study revealed that Lake Batur receives a considerable quantity of anthropogenic waste on an annual basis, including 14,776 tons of organic matter (COD), 1,486 tons of total nitrogen (TN), and 461 tons of total phosphorus. The primary source of these effluents was autochthonous effluents from FNC operations, which constituted 74.4% of the COD, 86.6% of the TN, and 85.6% of the TP. The distribution of effluents from community activities across the ECW, WCW, and MLW resulted in variability in the concentrations of total suspended solids (TSS), nutrients, chlorophyll-a (Chl-a), chemical oxygen demand (COD), total nitrogen (TN), total phosphorus (TP), and fertility levels in the nine LS. The Chl-a/COD ratio indicated that SL 1, situated in the ECW, exhibited the highest fertility, whereas SL 5, located in the MLW, demonstrated the lowest. The fertility level was constrained by phosphorus, as evidenced by a TP/TN ratio exceeding 12 in eight SLs. The Trophic Status Index (TSI) was calculated using Carlton’s formula, and the results indicated that, with the exception of SL 2, which was categorized as mesotrophic, the remaining eight SLs were eutrophic. Given that the Trophic Status Index (TSI) (Chl-a) is greater than the TSI (TP), it can be reasonably concluded that phosphorus is the limiting factor for algal development in seven of the nine SLs. The TSI (Chl-a) values for some SLs (SLs 2-4) were observed to be lower than the TSI (SD) values, indicating that non-algal particles may have exerted a greater influence on lake water clarity.