Abstract: Background and Objective: Maninjau lake is one of the important locations for aquaculture activity for many local people in Indonesia. The objective of the current research was to estimate the Nitrogen (N), Phosphorus (P) and Total Organic Matter (TOM) before and after fish mass mortality in Maninjau lake. Materials and Methods: This research was conducted in February, 2017, four months after mass mortality occurred. Nile tilapia (Oreochromis niloticus) and Common carp (Cyprinus carpio) mortality were occurred in August and September, 2016. Data were collected from four stations on Maninjau lake (Muko-Muko, Pasa, Pandan and Sungai Tampang). Water samples were taken from the surface (depth 0.1 m) and under floating net cages (depth 30 m) at each station and analyzed for N, P and TOM content. Water quality data taken in February, 2016 was used as a comparison. The differences between N, P, TOM, Particulate Organic Matter (POM) and Dissolved Organic Matter (DOM) levels before and after fish mass mortality were analyzed using a student t-test. Any differences between stations were analyzed using one-way ANOVA was performed using SPSS computer software. Results: The levels of N and P before and after fish mass mortality were significantly different (p<0.05). The N levels at surface ranged from 1.83-2.30 mg L–1. At 30 m, N levels ranged from 2.11-2.60 mg L–1. The P levels ranged from 0.50-0.91 mg L–1 and 0.81-0.92 mg L–1 at 0.1 and 30 m depths, respectively. The N level tended to the limiting factor for algae growth at each station (all N/P<16). The TOM levels before and after fish mass mortality ranged from (Mean±SD) 4.55±0.02-16.33±0.01 mg L–1 and 6.97±0.72-19.04±0.04 mg L–1 at 0.10 and 30 m depths, respectively. Conclusion: The availability of N, P and TOM in the water was significantly higher (p<0.05) after fish mass mortality and had a negative effect on the water quality of Maninjau lake.