Lake Batur’s water quality on Bali Island has significantly declined, leading to massive annual fish mortality rates. The suspected reason is the expansion of aquaculture using floating net cages (FNC) beyond their capacity. The study aims to assess the impact of FNC-based aquaculture on water quality and organic matter distribution, specifically total organic matter, TSS, and chlorophyll a. The result states that Lake Batur has exceeded its carrying capacity of 10,047 plots since 2018 and currently holds 18,768 plots as of 2022. Within the last five years (2018-2022), the FNC discharged 5,947 tons of organic waste into Lake Batur, containing 1,779 quintals of nitrogen and 430 quintals of phosphorus. Consequently, each liter of Lake Batur water accrues 7.29 mg of organic waste annually, including 2.18 mg of nitrogen and 0.53 mg of phosphorus. Organic waste in Lake Batur has led to a reduction in water transparency, an increase in total organic matter (TOM), a decrease in dissolved oxygen (DO), and an increase in chlorophyll-a (Chl-a) concentrations. Its changes serve as indicators of eutrophication and degradation of water quality. The distribution of organic matter across the euphotic zone did not correlate with FNC distribution, suggesting that FNC distribution no longer influences organic matter distribution. Environmental factors surrounding the SL have emerged as the primary driver of differences in organic matter distribution. It demonstrates the dissemination of organic matter in the euphotic zone of Lake Batur due to the constant discharge of effluent by the long-standing FNC, which has surpassed its maximum capacity.