Spatial variability of three benthic indices for marine quality assessment in a subtropical estuary of Southern Brazil

•We presented a congruence test for the biotic indices AMBI, BENTIX and M-AMBI.•Spatial variation of macrofaunal assemblages influenced the indices performances.•Only AMBI was congruent with physical–chemical proxies of contamination.•Ambiguous responses indicated additional effects of natural organic inputs.

Indices based on macrobenthic responses to disturbance remain to be adequately tested for the detection of spatial variability by robust sampling designs. We present herein a congruence test to real-world data of the widely used indices AMBI, M-AMBI and BENTIX in tidal flats of a subtropical estuary. We used a hierarchical sampling design to evaluate the spatial variability of the indices in response to distinct levels of sewage contamination. Indices were then tested for correlations with chemical proxies of contamination and for the similarity of responses. BENTIX and M-AMBI produced over- and underestimations of ecological status. We found a low degree of similarity among indices as an expression of the spatial variation of macrofaunal assemblages on their performances. Only AMBI varied at the contamination scale (103 m) and was congruent with physical–chemical proxies. Ambiguous responses indicated effects of natural inputs of organic matter rather than environmental quality associated to sewage.