Papaya, Nasugbu is situated in Batangas and is located at the entrance of the Verde Island Passage (VIP), a marine corridor with high biodiversity. This study aimed to obtain baseline information on substrate cover and biodiversity of three Marine Protected Areas (MPAs) in Papaya, Nasugbu and store the information in a database and publicly accessible website. Among the MPAs, Santelmo had the highest coral cover at 50.28% (Category A), followed by Pico de Loro at 18.65% (Category D) and Etayo at 13.41% (Category D). Among the three MPAs, Etayo had the highest macroalgae cover at 17.86%, while the other two MPAs had low macroalgae cover. In terms of biodiversity, Santelmo had the highest biodiversity with 22 hard coral genera (Category B), succeeded by Etayo which had 18 genera (Category D), and Pico de Loro which had 7 genera (Category D). The dominant coral genera were as follows: Pico de Loro (Porites sp.—11.62%, Millepora—1.66%, Acropora—0.71%); Santelmo (Porites rus—18%, Porites sp.—18%, Porites cylindrica—5%); Etayo (Porites sp.—4.57%, Millepora—1.01%, Galaxea—0.99%). The stitched images, substrate cover data, biodiversity data and geocoordinates for each MPA were uploaded into a database that was connected to a front-end website accessible to public users.