Anthropogenic activities are degrading coastal marine ecosystems globally. While the ecological and biodiversity implications of some of these impacts are well understood, for others there is a need for a greater understanding of the effects of these activities on vulnerable sedentary species. For researchers to pragmatically assess impacts on cryptic sponge species in highly productive reef systems, taxonomic assignment of these taxa is essential. With regards to the sponge fauna of Aotearoa, New Zealand, identification of sponge species is crucial for two main reasons. Firstly, these species significantly contribute to the productivity of inshore coastal reef ecosystems. Secondly, the existing literature of New Zealand’s sponge species has scarcities in species characterisation and identification for inshore sponge fauna. The Taranaki region is arguably foremost for consideration, as the coast would likely reflect any shifts in trans-Tasman current systems, and this region has a highly exposed geomorphology making it logistically difficult to conduct dive surveys. Furthermore, little is currently known about shallow water biogeography from this region. Focusing on temperate rocky reefs in the Taranaki Region of New Zealand, this thesis investigates the biogeography of sponge assemblages across broad spatial scales (hundreds of kms). It examines ecological processes, linked to trophic cascades to further our understanding of factors affecting the distribution and abundance of sponge communities at smaller spatial scales (tens of kms), with particular focus on the effects of land derived catchment discharges. A combination of Linnean taxonomic classification and operational taxonomic units (OTUs) were used to identify sponge species and highlight locations with unique assemblages of taxa at regional scales. To achieve this a program of taxonomic revision was required, including the redescription of a collection of common sponge species Aaptos globosa, Acanthoclada prostrata, Biemna rufescens, Halichondria (Halichondria) moorei, and Stylissa haurakii. These results progress the modern requirements of these species description from those described in early New Zealand literature that lacked adequate and detailed descriptions and in situ images. As a precursor to the Taranaki ecological survey, a revision of sponge species from the Bay of Plenty was conducted. This study examined the family Dysideiidae and describes two novel sponge species (Dysidea tuapokere and Dysidea teawanui), from Tauranga Harbour, in the Bay of Plenty, and validated five species within New Zealand’s Exclusive Economic Zone, Dysidea cristagalli, D. hirciniformis, D. navicularis, D. ramsayi, D. spiculivora. Dysidea fragilis is now considered to be invalid, and D. elegans is considered unrecognisable. Further taxonomic assignment of Taranaki sponge fauna is required and is ongoing. The set of qualitative, but validated data now provides a baseline survey of spatial heterogeneity in terms of the distribution of sponge taxa across the Taranaki and central west coast North Island region. Biogeographic data showed that the geographic range of sponge species is highly patchy and supports the hypothesis that species assemblages at the Pariokariwa Reef (now part of the Parininihi Marine Reserve) are highly unique. Results from this investigation provide a baseline species diversity estimate within Taranaki and reveal Waitara reefs as biologically significant areas with the second largest number of unique sponge species out of all six locations surveyed. These findings have important implications for developing conservation strategies for marine fauna in Taranaki, highlighting locations of significant biological diversity, abundance, and uniqueness. Potential drivers for this biogeographic patchiness are addressed in subsequent sections of the research program. Environmental factors influencing the distribution and abundance of marine sponges as described around the Taranaki region (Waitara reefs, Waiwhakaiho reefs, and Hangatahua Reef) over a three-year period were examined. There was a greater diversity and abundance of sponges at rocky reef stations that were in closer proximity to river mouths. This provides evidence that terrestrially derived organic matter from rivers may be supporting a greater assemblage and biomass of marine taxa on coastal rocky reefs, despite the increased sediment input from some of the catchments examined. The size of sponges in terms of volume were greater at coastal stations positioned next to rivers with a relatively large coverage of indigenous forests as opposed to reef systems adjacent to modified and urbanized catchments. An examination of the effects of several physico-chemical factors including turbidity, total phosphorus, total nitrogen, and Escherichia coli presence (an indicator of human and agricultural inputs), revealed that sponges appear to be resilient to certain degrees of exposure to these variables. There appears to be a negative correlation between effects of turbidity and nutrient level on sponges generally, with high levels of turbidity associated with decline in sponge characterised reef habitat. In contrast, some sponge species appear to thrive in turbid conditions that have high levels of nutrients in a form that they can profit from metabolically. Therefore, the quality of the catchment system can directly influence the quality of the nearshore benthic sponge assemblage. Finally, the critical role of marine sponges in processing terrestrially derived carbon was investigated by examining the proportional contribution of food from various sources to the diet of sponges on temperate rocky reefs. Our isotope analysis revealed that marine food sources including coastal seston (>1.2–400 µm), coastal GFX (combined fine and coarse glass fibre filter samples >0.7–1.2 µm), and coastal bacteria (>0.2–0.7 µm) contributed the largest proportion to the diet of coastal sponges at 60–73% across our three stations. This was followed by a relatively large proportion of terrestrially derived food sources including freshwater seston (>1.2–400 µm), freshwater GFX (>0.7–1.2 µm), and freshwater bacteria (>0.2–0.7 µm) at 27–40%. Sponges are therefore argued to play significant roles in linking terrestrial and marine food webs, and associated carbon cycles, via recycling terrestrially derived carbon and nitrogen. Combining our estimated C retention rate with the isotopically-determined contribution of foods from terrestrial sources to the diet of coastal sponges (27–40%), suggests that sponge meadows may retain approximately 117–173 kg of terrestrially-derived C km−2 day In summary, the biogeographic distribution of sponge fauna that characterise nearshore reef environments around the Taranaki region has been described at large and small scales. This provides a baseline for future surveillance of nearshore ecological condition over ensuing years. This study highlights the importance of undertaking taxonomic precursor studies of regional sponge fauna to allow researchers to gain the taxonomic expertise to conductor wider scale ecological studies of this diverse phylum. The distribution of assemblages in Taranaki is particularly patchy with several highly unique communities being identified. These findings are important to the management of sponge fauna and the systems that support them. Land-based activities and ground cover and use are having direct effects on coastal reef communities, as seen in the distribution, abundance, and sizes of sponge species over large-scale environmental gradients. An important role of sponges in processing terrestrial derived carbon has been identified. The implications of this are that sponges are ingesting terrestrially derived organic matter on temperate reefs and potentially turning it into sources of food in the form of biomass, and cell shedding. This study shows that rivers and their derived food sources are important for coastal sponge communities. A unique assemblage of sponges was found close to a catchment system that discharges large quantities of sediment from significantly degraded hinterland suggesting that some taxonomic groups can thrive in areas where other species may struggle hence, species specific studies of how certain taxa adapt to multiple environmental stressors is suggested. Future studies should endeavour to further this research and expand our current understanding of sponge fauna as they constitute useful sentinel organisms.