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Marine activities may cause the degradation of coral reefs. The composition of benthic communities and seawater quality have been commonly used as the proxies to assess the impacts of marine activities. However, these proxies may not be able to detect the subtle differences within homogeneous environment. We used photogrammetry to quantify the subtle differences of structural complexity between heavily and lightly trafficked sites at Wanlitong, southern Taiwan. Our study demonstrated that the impacts of marine activities can be detected within tens of meters through quantifying structural complexity of coral reefs. Vector ruggedness measure (VRM) is a more suitable metric than conventional linear rugosity to detect such impacts. The correlations between structural complexity and coral cover have variances while comparing with previous studies. The results show that using photogrammetry to quantify the structure of coral reefs can provide a novel aspect to evaluate the subtle differences caused by marine activities. • Using 3D photogrammetry to assess the impacts of marine activities. • Differences of structural complexity of coral reefs can be detected within distance of tens of meters. • Structural complexity may not be correlated with coral cover in shallow water reefs. • Vector Ruggedness Measurement is a better metric to detect subtle differences on coral reefs. [ABSTRACT FROM AUTHOR]