Six benthic biotic indices (Shannon–Wiener H′log2, W-statistics, BOPA, BENTIX, AMBI and M-AMBI), based on different ecological principles, were applied to assess the health of variously disturbed tropical intertidal habitats of the Port Blair coastline. A total of 243 replicate samples were collected during the dry period (January, February and March) of 2014–2016. Temperature, salinity, dissolved oxygen, sediment pH, total organic matter content and texture were analysed. A high mean abundance of opportunistic species (Orbinia sp. 748, Capitella singularis 237 and Armandia sp. 114 ind. m−2) was observed at Phoenix Bay, a gradual decline in diversity at Junglighat and a comparatively high diversity and moderate biomass at Wandoor, reflecting a human pressure gradient. Results showed an annual decline of benthic quality from 2014 to 2016 (good to moderate). Overall BOPA failed to distinguish the magnitude of disturbances, while the rest of the indices classified the benthic quality from undisturbed/high (WD), slightly disturbed/good (JG), to moderately disturbed/moderate to poor (PB). The subjective analysis demonstrated that the urban centres corresponded to disturbed benthic communities of dominant first and second order opportunistic species, while sensitive (EGI) and indifferent (EGII) were associated with the least disturbed or undisturbed site. The study successfully demonstrated the performance of temperate indices in intertidal habitats against the mild organic enrichment. However, for an effective assessment, setting natural reference conditions and sampling in stable dry periods (strong seasonality in tropics) is desirable. In order to test the performance of biotic indices, a long-term monitoring approach of taking abiotic and biotic descriptors into account is recommended.