This study introduces the hybrid of the Bayesian optimization algorithm and support vector regression (BOA-SVR) models to predict the removal of aerobic organic (total chemical oxygen demand, COD) and nitrogen compounds such as total Kjeldahl Nitrogen (TKN), ammonium nitrogen (NH4-N), and nitrate nitrogen (NO3-N) from municipal wastewater in a gas-liquid-solid circulating fluidized bed (GLSCFB) bioreactor. GLSCFB bioreactors treat wastewater by removing nutrients biologically. The downer of a GLSCFB bioreactor provided experimental data on TKN, NH4-N, NO3-N, and TCOD removal. The hybrid optimal intelligence algorithm (BOA-SVR) has improved model accuracy across multiple domains by combining BOA and SVR. The coefficient of determination (R2), residual, mean absolute error (MAE), root mean square error (RMSE), and fractional bias (FB) were used to analyze BOA-SVR model performance. The models match experimental data from four operational stages well, with R2 or adj R2 values above 0.99 for all responses. The model's accuracy was confirmed by relative deviations and residual plots showing dispersion around the zero-reference line. The BOA-SVR model consistently predicted dependent variables with low RMSE and MAE values (≤ 2.24 and 2.21, respectively) and near-zero FB. Computing efficiency was shown by optimizing TCOD, TKN, NH4-N, and NO3-N models in 70.61, 72.89, 74.37, and 54.07 s. A rigorous test on unseen data with different noise levels confirmed the model's stability. Furthermore, BOA-SVR performs better than traditional multiple linear regression (MLR). Overall, the BOA-SVR model predicts biological nutrient removal in municipal wastewater utilizing a GLSCFB bioreactor quickly, correctly, and efficiently, reducing experimental stress and resource use.