Here is a review paper on bacterial bioindicators in general:
Sumampouw OJ, Risjani Y. 2014. Bacteria as indicators of environmental pollution: Review. International Journal of Ecosystems 4(6): 251-258.
And this paper is more specific to lagoons:
Hedouin L et al. 2008. The tropical brown alga Lobophora variegate as a bioindicator of mining contamination in the New Caledonia lagoon: A field transplantation study. Marine Environmental Research 66: 438-444.
Are you looking for an indicator of some particular kind of pollution? A classic bacteria used for domestic and fecal matter is E. coli, and it is easy to detect and measure. It is associated to sediments at lotic wtlands, too.