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A planned artificial reef (AR) deployment program as part of a fisheries enhancement might be a useful tool for managers to supplement traditional ways to utilize available space and augment local productivity. Several AR deployment initiatives have been carried out globally, but they are rarely subjected to a rigorous site selection process. We created a site selection procedure in this study that includes systematic stages including exclusion mapping, underwater visual transect, benthic composition, seawater quality, and comparative visual mapping. This research focused on restoring the fishing grounds for artisanal fishermen by deploying AR along the southeast coast of India. The results of each stage in the procedure enabled us to choose suitable locations at a target depth with low wave action, no slope, and a good substrate capable of supporting an AR. Analysis of variance (ANOVA-one way) showed significant (p < 0.05) spatial variation for depth, slope, seawater current, salinity, chlorophyll-a, benthic density, and diversity. The geographical information system (GIS) based model output showed space allocation for AR deployment. The GIS methodology for site selection was developed to be easily adaptable to the demands of diverse artificial reef programs. The integrated strategy has proven to be a successful regulatory intervention for AR deployment practices in order to facilitate coastal restoration and management.