The predominant aim of the current research was to generate a proposal for the removal of arsenic, a highly toxic pollutant, encountered within the Papallacta Lagoon in Ecuador. The average concentrations of As yielded ranges between 18 to 652 μg/L, through the use of metallic nanoparticles. Sampling was performed in the lagoon with their respective geographic locations and “in situ” parameters. Nanoparticles of Mn3O4 NPs, Fe3O4 NPs, and CuO NPs were synthesized at a 0.5 M concentration, using the precipitation method, and borojó (Borojoa patinoi) extract was added as an anti-caking agent as well as antioxidant. The nanoparticles were characterized by visible spectrophotometry, scanning electron microscopy (SEM), transmission electron microscopy (TEM), X-ray diffraction (XRD), and Raman spectroscopy. After arsenic removal treatment using nanoparticles, a randomized experimental design of different concentrations (5 mg/L, 10 mg/L, 25 mg/L, 50 mg/L, 100 mg/L, and 150 mg/L) was applied at laboratory level. The average diameter of Fe3O4NPs ranged from 9 nm to 36 nm, Mn3O4 NPs were 15–20 nm, and CuO NPs ranged from 25 nm to 30 nm. Arsenic removal percentages using Fe3O4 NPs with a concentration of 150 mg/L was 87%; with Mn3O4 NPs, the removal was 70% and CuO NPs of about 63.5%. Finally, these nanoparticles could be used in a water treatment plant for the Papallacta Lagoon.