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Novel approaches for monitoring coastal water quality changes and identifying associated contaminant source(s) are of growing importance as climate change and population redistribution to coastal zones continue to impact coastal systems. CrAssphage, a virus found in the human gut and shed with fecal matter, is currently gaining popularity as an indicator of human fecal contamination in surface water and groundwater. Here we demonstrate that DNA assays targeting crAssphage genetic fragments can be used to detect pollution from nearshore onsite wastewater treatment systems discharging to the ocean via submarine groundwater discharge. We integrated this novel viral monitoring tool into a field study that characterized the physical hydrogeology (hydraulic gradients, hydraulic conductivity, and seepage fluxes) and surface water and groundwater quality at a study site on the north shore of Nova Scotia, Canada. Increased use of onsite wastewater treatment systems during the summer cottage season coincided with widespread detections of crAssphage in submarine groundwater discharge (4/4 samples) and coastal surface waters (3/8 samples). Conversely, classical fecal pollution indicators based on bacterial targets (Escherichia coli and human-specific Bacteroidales genetic marker (HF183)) were sparsely detected in the samples in the coastal environment (2/12 E. coli samples, 0/12 HF183 samples), likely due to greater attenuation of bacterial contaminants within the subsurface environments. Results from this first application of crAssphage in coastal groundwater contribute to a growing body of research reporting the application of this emerging tracer in various environments impacted by sewage pollution sources.