Wetlands are an important feature for our society that provides versatile benefits, such as habitat for diverse wildlife, shoreline erosion protection, flood control, and mitigation of climate change through capture and storage of carbon. The aim of this work was to assess the application of nanotechnologies for the restoration of the water quality in the Cascajo Wetlands, Peru, where the water quality was deteriorated. Ceramic-based bio-filters (CBBFs) were used to reduce and buffer the contamination rates of pollutants, whereas micro-nano bubbles (MNBs) were applied to increase the dissolved oxygen and release free radicals in water. Additionally, bio-fence was implemented to prevent water intrusion from the ocean. Remote sensing data through the Normalized Difference Vegetation Index (NDVI) and the Enhanced Vegetation Index (EVI) was used to monitor the water surface condition. With treatment of CBBFs and MNBs for 13 months, we observed reduction in the chemical oxygen demand (COD), biological oxygen demand (BOD), total nitrogen (TN), and total phosphate (TP) in the water body, showing removal percentages of 98.5%, 97.5%, 98.1%, 98.5%, and 94.6%, respectively, in comparison with values before starting the implementation. The trends of NDVI and EVI over seasons are not completely aligned with the results taken from the wetlands treated with MNBs, CBBFs and bio-fence. While TN was highly correlated with the empirical value of TN based on remote sensing, no correlation was observed between COD and empirical COD. The use of eco-friendly techniques has performed efficiently to remove the pollutant.