An environmental monitoring programme was initiated by Meridian Energy in 1997 to gather information pre and post the introduction of 2MTT to assess the effects of the expected increase in tailrace discharge in Doubtful Sound. This programme used permanent transects to monitor abundance of indicator species, and abundance and height of black coral. The distribution of selected indicator species has been monitored using permanent horizontal transects at 10 sites in Doubtful Sound and three in Milford Sound annually (except 2012). Divers assessed these transects. Results show no temporal change at Milford Sound, outer Doubtful Sound, and all but one of the inner Doubtful sound sites. In addition, differences among the areas in term of total abundances was evident. Overall, the presence of indicator species throughout Doubtful Sound suggests that conditions have not changed sufficiently to influence the indicator’s distributions and abundances. However, black coral numbers and health at one of the inner Doubtful sound sites need to be monitored closely in future surveys.