The functional dynamics within bacterial communities are increasingly recognized as crucial to cultured fish and shellfish health. Interest in microbiome analysis has soared in response and a number of studies on environmental, gut, and skin bacteria have been conducted within aquaculture contexts. The majority of investigations use NGS platforms to sequence the hypervariable V3/V4 region of the bacterial 16s rRNA gene, providing identification and relative abundance data for all genera. While the V3/V4 region can also provide species-level differentiation in some cases, the necessary resolution for accurately defining closely related species or detecting uncommon or recently identified genera is lacking. Bacterial metabolism, growth strategies, pathogenicity, and capacity for beneficial or antagonistic microbial interactions are broadly species dependent. The work presented here represents a compilation of data from our custom full-length (FL) 16S rRNA gene sequencing platform and database. We describe species-specific bacterial functions related to nitrite and salinity tolerances in nitrifying biofilms of recirculating aquaculture systems (RAS), along with sulfur and iron-metabolizing bacteria profiles that inform on biofilter performance. We find that full-length 16S rRNA identification of important bacterial groups such as Vibrio is key to avoid overrepresenting health risks from benign species, while identifying those that are truly threatening. Further overrepresentation of production risks due to some secondary metabolites (toxins, taste and odour chemicals) produced specifically by cyanobacteria and myxobacteria have been detected, which can blur data interpretation and management decisions. Lastly, probiotic retention within treated animals and environments can be misrepresented due to failures in differentiating common non-therapeutic members of the probiotic genus. These examples and others will display the scientific value of full-length 16S rRNA sequencing in RAS biofilter function, water quality surveillance for indoor and outdoor aquaculture, pathogen profile identification, and investigations of probiotic efficacy, all of which are relevant to critical management decisions for aquaculture producers.