Very few coral reefs are located close enough to large cities to study the influence of large urban populations on reef assemblages. An exception is the Thousand Islands reef complex to the north of Jakarta, the capital city of Indonesia, and one of the largest conurbations in the world. Here we present data from a detailed survey where sponge assemblages were assessed at 30 patch reefs associated with islands in three coastal zones along an in-to-offshore gradient. Sponge assemblages are described at three taxonomic levels of detail (species, genus and family level). We recorded a total of 118 sponge species, 64 genera and 36 families, Aaptos suberitoides (Brønsted, 1934), Clathria (Thalysias) reinwardti (Vosmaer, 1880), Petrosia (Petrosia) nigricans (Lindgren, 1897) and Xestospongia testudinaria (Lamarck, 1813) were the most common species overall. There was a pronounced difference in composition among zones with the most distinct difference between the inshore zone and the other two zones. The inshore environment was characterised by very high turbidity and low live coral cover; the dominant substrate consisted of algal turf and sand. Environmental conditions improved and sponge diversity increased further offshore, although most areas appeared to have been affected by some form of disturbance. Ordinations were also largely congruent, at species, generic and family levels of taxonomic resolution. This indicates that variation in composition at higher taxonomic levels is a good indicator of variation at lower taxonomic levels, at least when there is a pronounced environmental gradient.