The townships of Longos and Talaba in Cavite served as the main location for the world of Putot. A big part of the towns hang on stilts on Manila Bay, where most of its residents farm mussels. With the help of the townspeople, the production staff and crew created Putot's world.

The film was given a mysterious, greenish hue to echo the water that always surrounds them. DOP Alma dela Pena with just six lightbulbs and plenty of sun managed to create an above-ground waterworld. Production Designer CD Dy managed to create beauty in such a poverty-stricken place, reflective of Putot's view of his own world.

The heart of the movie is the friendship between two leads, Putot and Mayang. First-time actors Carl Taylan and Karen Pilapil were cast after a long round of auditions. Memorable cameos by Meryl Soriano (Room Boy) and Nor Domingo (Big Time) also helped the younger actors along.

Production began first week of 2006 and wrapped in three days. Additional scenes were shot a few months later. Arnold Buena provides the lush music.