In this study, we proposed a sustainable practice for managing an environmentally friendly outdoor earthen ponds for shrimp biomass production based on biological nitrogen treatment processes. A 26-day bottom soil acclimation was operated under appropriate oxygen (> 5 mg/L) and alkalinity (100–150 mg-CaCO3) concentrations, followed by a 76-day Penaeus vannamei cultivation in small (0.04 ha; pond I) and large (0.16 ha; pond II) ponds without water exchange and the addition of probiotic bacteria. With the proper pond preparation, the nitrification process was promoted during the pond acclimation period, as demonstrated by the conversion pattern of total ammonia nitrogen (TAN) oxidation to nitrite. During shrimp cultivation, the acclimated ponds were able to control TAN and nitrite concentrations below acceptable limits (< 0.2 mg-N/L) while the TAN build-up was reported when the feeding rate exceeded 220 kg-feed/ha/day, indicating the limitation of the nitrogen waste carrying capacity. Additionally, pond acclimation encouraged bacterial activities, especially assimilation and nitrification processes, with higher rate indices of TAN removal (0.048–0.069 g-N/m2/h) compared to photoautotrophic uptake (0.014–0.028 g-N/m2/h). The overall TAN carrying capacity was extrapolated to be 1.31–2.00 g-N/m2/day. Biological treatment processes all contributed to low dissolved inorganic nitrogen (DIN) accumulation (4.8–6.0%) and high unidentified nitrogen loss (54.7–59.3%). The pond ecological balance also promoted phytoplankton growth at chlorophyll-a concentration of 122.34–169.66 mg/m3. Oxygen evolution index by photosynthesis (2.65–2.98 g-O2/m2/h) was sufficient for the consumption of both water (1.85–1.96 g-O2/m2/h) and bottom soil (0.09–0.12 g-O2/m2/h); however, mechanical aeration was necessary during a light absence period due to lower rate of extrapolated daily photosynthesis (31.81–35.81 g-O2/m2/day) compared to the respiration rate indices of water and bottom soil (45.88–47.57 g-O2/m2/day). High shrimp production of 7.9–9.2 t/ha/crop was achieved with the average daily gain (ADG) of 0.29–0.31 g/day and the feed conversion ratio (FCR) of 1.13–1.28. These findings contributed to the strategic development of pond acclimation and the sustainability of outdoor earthen shrimp ponds in terms of both ecosystem balance and the profitability of high biomass production.