Aim This study set out to determine whether phage-based indicators may provide a ‘low-tech’ alternative to existing approaches that might help maintain the microbial safety of shellfish and their overlying waters. Methods and Results Mussels and their overlying waters were collected biweekly from an estuary in southeast England over a 2-year period (May 2013–April 2015) (n=48). Levels of bacterial indicators were determined using membrane filtration and most probable number methods and those of bacteriophages were determined by direct plaque assay. The detection of adenovirus was determined using real-time polymerase chain reaction. The results revealed that somatic coliphages demonstrated the most significant correlations with AdV F and G in mussels (ρ=0·55) and overlying waters (ρ=0·66), followed by GB124 phages (ρ=0·43) while Escherichia coli showed no correlation with AdV F and G in mussels. Conclusion This study demonstrates that the use of somatic coliphages and GB124 phages may provide a better indication of the risk of adenovirus contamination of mussels and their overlying waters than existing bacterial indicators. Significance and Impact of the Study Phage-based detection may be particularly advantageous in low-resource settings where viral infectious disease presents a significant burden to human health.