Sponges play a vital role in the world's most complex and vulnerable marine ecosystems. Various in situ studies have suggested that sponge morphologies (developed from exposure to a range of biophysical factors) can be considered as ecological indicators to current detrimental environmental changes such as climate change, overfishing, pollution and dredging for coastal development. Regional and long-term taxonomic data on sponges within each geographic range is not always available, especially from the Great Barrier Reef (GBR), due to dearth of sponge research. In this study, to understand large-scale variation and advance sponge research and knowledge, morphological characteristics were adopted as a rapid practical way to identify sponges from photo-transect images of a long-term dataset from the GBR. Biennial surveys were carried out in 2008–2014 from 28 pairs of take and no-take zones of the GBR. To evaluate the temporal changes in sponge morphology and correlation between abiotic factors, remote-sensed data such as chlorophyll a, current, wave height and sea surface temperature (SST) during the survey period were analyzed. Results showed sponges were ubiquitous in all six surveyed locations and their distribution was spatially heterogeneous. Encrusting forms were dominant followed by upright, massive, cups and tabular growth forms. Sponges were more prevalent in Innisfail, Pompey and Townsville compared to Cairns, Swain and Capricorn Bunker. Biennial observations showed greater sponge coverage in 2010 and 2014, especially in the central GBR, which may be related to the geomorphology and habitat of reefs along with its influence by wind and wave action. Also, the aftermath of Cyclone Hamish (2009) and Yasi (2011) would have triggered suspended particulate matter that are beneficial to sponge growth. Geostrophic current showed a weak relationship on encrusting, upright and massive forms, whereas, chl-a, wave height and SST appeared to have no effect on sponge morphology, suggesting sponges may be resilient to adverse conditions in the GBR. Whilst selected sponge morphologies can act as environmental proxies to monitor adverse conditions, further in situ research on other environmental parameters such as turbidity, sedimentation, cyclone, tides are required to bring substantial conclusions on sponge morphologies as ecological indicators.