Coastal communities of Tanzania use natural water systems such as rivers, estuaries and 64 marine for various activities like drinking, fishing, washing and bathing. However, there is scanty information on the safety for these water bodies for the various uses. In this study faecal indicator bacteria were assessed in three sites along the coast of Tanzania (i.e. Pangani Estuary in Tanga Region, Ruvu Estuary in Pwani Region and Mzinga Creek in Dar Es Salaam Region). At each site, three sampling stations covering fresh, brackish and marine waters were selected for monthly sampling between July 2009 and June 2010. Faecal bacterial indicators were generally higher in Mzinga Creek compared to the rest of the study sites with significant differences between Mzinga Creek and Pangani Estuary for total coliforms (TC) and faecal coliforms (FC) (P < 0.05). All faecal indicator bacteria were significantly higher in fresh waters compared to brackish and marine waters (P = 0.0001), for TC and FC and P = 0.001 for Enterococcus (ENT). The faecal indicator bacteria correlated positive to each other and negatively to some environmental parameters namely pH and Salinity. Results suggest allochthonous sources of contamination and the influence of environmental factors. Generally the faecal bacterial indicators in the studied waters along the coast of Tanzania were within the acceptable standards according to WHO and USEPA indicating low risks situation for recreational purposes. However, these levels of faecal bacteria does not warrant the use in the studied estuaries for shellfish harvesting and the fresh water is not suitable for direct drinking. Further studies and monitoring programs are recommended to substantiate the current results.