Inland aquaculture in Peru has experienced continuous growth, leading to intensive use of water resources and the discharge of effluents that pollute water bodies. This research proposes a new biotechnological perspective by evaluating, for the first time under laboratory conditions, the application of Nostoc cf. sphaericum as a phytoremediation agent for fish farming waters from the Huaylacancha Lagoon (Junín, Peru). Initially, the cyanobacterium was morphologically characterized, belonging to the genus Nostoc, with an oval shape, a brown-gold-olive color, a gelatinous texture, vegetative cells measuring 6×6 µm, and heterocysts measuring 7×6 µm. Subsequently, a 2³ factorial experiment was conducted considering lighting (1500, 3000 lux), photoperiod (12, 24 hours), and initial biomass (20, 40 g). The physicochemical characterization of the lagoon water samples averaged: nitrates 1.92 mg/L, phosphates 0.9 mg/L, pH 8, DO 5.4 mg/L, TDS 218 ppm, EC 277 µS/cm, and temperature 12.1°C. The ANOVA for nitrates revealed interaction effects between biomass and photoperiod, and between biomass and phycoremediation period (p ≤ 0.05), reaching 1.09 mg/L under 24 h of light with 20 g of initial biomass, and 0.78 mg/L after 16 days with 20 g. Phosphates showed an effect of the phycoremediation period (p ≤ 0.05), reaching 0.07 mg/L after 8 days of phycoremediation. DO showed significant interactions between light intensity and biomass, photoperiod and phycoremediation period, and biomass and phycoremediation period, reaching a value of 12.75 mg/L in 12 days with 12 h of light. Nitrate removal reached 59.4% with an initial biomass of 40 g, while phosphate removal reached 55% after 16 days of phycoremediation. The cyanobacterium Nostoc cf. sphaericum significantly reduces phosphate and nitrate levels in fish farm waters and exhibits phycoremediation potential for other types of contaminated water.