- Abstract Disease outbreaks are a major concern in aquaculture. This is particularly true in intensive recirculating aquaculture systems (RASs), due to the high rearing densities in a system where high concentrations of organic matter are produced with minimal water exchange. This study assessed the survivability of the common fish pathogen Streptococcus iniae in a solid-removal unit of a RAS, the upflow anaerobic sludge blanket (UASB). A PCR detection method, along with an improved protocol for the extraction of high-quality DNA from sludge samples, were utilized for this purpose. This method enabled detection of S. iniae at a minimum concentration of 7.6 × 10 5 CFU mL − 1 raw sludge. We examined the survivability of S. iniae in batch digesters, which consisted of sealed serum bottles filled with sludge from the UASB reactor, and in laboratory-scale flow-through UASB reactors that were continuously fed with fish waste sludge. Results demonstrated a gradual decrease in the intensity of the PCR-amplified product to the point of no detection in either batch or UASB digesters, suggesting that the conditions present in the UASB reactor are not favorable for S. iniae . The PCR-based detection method was successfully applied to sludge from a commercial RAS enabling detection of potentially pathogenic bacteria. Statement of relevance The manuscript addresses the control of bacterial disease-causing agent in a near-zero discharge aquaculture system which contains a novel solid removal unit. The bacteria studied is S. iniae , a significant disease-causing agent in aquaculture. The potential threat of disease outbreaks increases with the intensification of the culture system, such as the one described and analyzed in this study. This intensification is of high relevance to the industry, as it reduces environmental contamination due to fish production as well as enables fish culture in places distant from a natural water source.