El Nido, Palawan is one of the top tourist destinations in the Philippines with vibrant nature-and tourist-based economy. However, the impact of active tourism activities, and construction of tourism related establishments have caused de- cline in the water quality in Bacuit Bay. The sudden imposed lockdown and strict quarantine measures all over the country in March 2020 brought by COVID-19 outbreak halted the tourism industry in El Nido, Palawan. This study aims to determine the impact of shutdown of tourism industry in the water quality as well as perception of the local people on the natural environment of Bacuit Bay. Collection of water samples were conducted and analyzed for fecal coliform, oil and grease and nutrients such as phosphates and nitrate. This study also utilized the data from regular monitoring activities of the Palawan Council for Sustainable Development to evaluate the trends and changes on water quality from 2015 to 2021. Water quality showed improvement on the fecal coliform levels in three monitoring stations along Bacuit Bay, a year after the implementation of national and localized lockdown and shutdown of tourism in El Nido Palawan. Similarly, oil and grease, phosphates and nitrates were all within the Class SB guideline in April 2021. This result corroborated with the local people’s perception of water quality where less trash, noise, light and presence of fishes were observed. This research documented the perceived environmental improvement during the lockdown and shutdown of tourism activities and provides data and information that can be utilized to plan post pandemic measures to build the tourism back better in El Nido, Palawan.