This study uses surplus production model-based methods to assess data-poor stocks and estimate key reference points for Atlantic bonito (Sarda sarda) and bluefish (Pomatomus saltatrix) in the Black Sea. Our results demonstrate that the catch maximum sustainable yield (CMSY) method, using catch data only, yields similar results to the more accurate Bayesian Schaefer model (BSM) method, fitted with commercial catch-per-unit-of-effort data, and therefore is suitable in assessing data-poor stocks. We explore the ecological impacts of the two stocks on other commercial species and compare impacts of predation and fishing. Prior to 1995, the consumption of bonito and bluefish on anchovy, horse mackerel, and sprat exceeded the removal of those prey species by the fisheries. Later on, the trends reversed, with catches of prey species becoming more than three times higher than their predation by bonito and bluefish. Horse mackerel, the main prey of bluefish, has declined to critical levels since 1995, which is likely contributing to the general decline in bluefish, along with overfishing. Heavy fishing of bonito and bluefish has caused their current depleted states and combined with their significant impact on prey fish contributed to the ecosystem regime shift in the Black Sea. Due to the present steady positioning of low stock regimes, the recovery of the two stocks need decisive and possibly prolonged rebuilding measures, including a reduction in fishing pressure, efficient control of under-sized catch, and ensuring sufficient prey biomass availability.