Background: A 5 Ci 241Am-Be radio isotopic neutron source-based prompt gamma neutron activation analysis (PGNAA) setup was designed for estimation of minimum detectable concentration (MDC) of elements in aqueous solutions. Materials and Methods: Performance variables related to PGNAA setup (source to sample distance, sample to detector distance and volume of water) were optimized experimentally. Characterization of the setup was done by chlorine and boron elements using sodium chloride (NaCl) and boric acid (H₃BO₃) compounds respectively. Results: PGNAA setup was calibrated for different concentrations of Cl and B in aqueous solution. The chlorine concentration was varied over 1.2 g/L, 2.4 g/L, 3.6 g/L, 4.8 g/L, 6.0 g/L and 7.2 g/L in water samples while boron concentration was varied over 0.1 g/L, 0.2 g/L, 0.3 g/L, 0.4 g/L and 0.5 g/L. The MDC of chlorine and boron were calculated for various characteristic prompt gamma energies. Estimated MDC of chlorine and boron are 175 ± 53 ppm at prompt gamma energy 6110 keV and 3 ± 0.95 ppm at prompt gamma energy 478 keV respectively. Conclusion: In the present work, PGNAA setup was developed and characterized for the in-situ analysis of aqueous solutions using a 5 Ci Am-Be neutron source. The chlorine concentration was varied from 1.2 to 7.2 g/L and boron concentrations were varied from 0.1 to 0.5 g/L. The setup shows linear response for both chlorine and boron for wide energy range. The obtained results were also compared with other previous published work. It shows good agreement with present results.