This study aims to improve water quality and reduce eutrophication downstream when receiving water from aquaculture facilities that can support the aquaculture industry and increase fish production capacity. The primary objective is to investigate a novel approach, using magnesium (Mg)-modified biochar water treatment systems from pinewood, to remove the main eutrophication agents (i.e., phosphorous and nitrogen) from the effluents of aquaculture facilities in Magic Valley, Idaho. The downstream water contains approximately 0.14 mg/L of phosphorous and 2.25 mg/L of nitrogen. The results show that the initial P2O5 concentration between Mg-modified and non-modified biochar is comparable. After exposure to aquaculture production water, the modified biochar is shown to have a significant increase in phosphorous and nitrogen adsorption. Non-modified biochar started with noticeably higher concentration levels of nitrogen than modified biochar. Over time in the treatment water, the modified biochar showed a significant increase in nitrogen concentration. Mg bonded to the modified biochar is shown to decrease drastically after exposure to the effluent. This could be due to the insufficient bonding of the magnesium to biomass feedstocks during pre-processing and biochar production. The amount of biochar near the end of experimentation is almost comparable to the non-modified char. We concluded that the proposed approach, using a Mg-modified biochar water treatment system, could sequester more nitrogen and phosphorous over time.