Shrimp farming has recently pursued systems that minimize the use of water. A biofloc technology (BFT) culture system contributes to water quality by removing nitrogen compounds, supplementing the shrimp diet and allowing for the use of high stocking densities. In addition, this system enables the culture with minimal water exchange. This study raised Litopenaeus vannamei shrimp in a BFT system at different water depths. Three treatments were compared at 0.40, 0.80 and 1.20 m of water depth (salinity 30). Treatments were randomly assigned to nine 35,500 L lined tanks in a greenhouse. Each tank was stocked with 14,000 animals (400 shrimp m− 2). Feed (38% crude protein - CP) was provided three times per day via feeding trays. The study lasted 120 days. The water quality parameters, weight gain, FCR and survival were evaluated. No significant differences were detected for water quality parameters (P > 0.05) except for alkalinity, which was higher in the 1.20 m treatment (P < 0.05). The final weight and survival did not show significant differences (P > 0.05). Final biomass (kg m−3) was significantly higher in the 0.40 m treatment (P < 0.05). The productivity levels were 2.88 (1.2 m), 4.83 (0.80 m) and 8.45 kg m− 3 (0.40 m) at 17 weeks. The 0.40 m treatment used 119 L of water to produce 1.0 kg of shrimp. Based on the results, decreasing the depth of the shrimp tanks to 0.4 m increases the productivity and decreases the use of water per kilogram of shrimp produced. Statement of relevance In the last few years, several researches have been developing technologies to improve Aquaculture production. Shrimp culture achieved high levels of productivities, mainly in semi intensive culture systems in subtropical areas around the world. However, environmental impacts and shrimp diseases have been worldwide spread. In addition, the effluent from aquaculture rich in organic materials and nutrients can cause environmental pollution as well as expenses with pumping water. Thus, the shrimp culture has been directed to biosecurity systems that minimize the use of water. The new proposed culture system, Biofloc Technology Culture Systems (BFT) is characterized by zero water exchange and super-intensive culture of shrimp in enclosed raceways. This system is considered environmentally friendly and avoids nutrient rich waste from polluting coastal waters. The nutrients transformation in biofloc (microorganisms) contribute to the water quality, through the removal of nitrogen compounds, supplements the shrimp diet and allows the use of high stocking densities. Depth as a factor in pond ecosystem management has been given little attention, despite its theoretical importance in autotrophic and heterotrophic systems. Besides of this, the shrimp behavior and water quality parameters could be completely changed according to the amount of water available in the culture system. Therefore, the objective of this study was to compare the growth performance of Litopenaeus vannamei in greenhouse-enclosed raceways with different depths, in BFT culture system. According to the results, water quality parameters were within recommended ranges for shrimp health in terms of dissolved oxygen, pH, temperature and salinity in different depths. The same was detected for nitrification process. Anyway, the amount of water used to produce 1.0 kg of shrimp ranged from 119 to 352 L. The best result was in 0.4 treatment with the production of 8.45 kg m− 3. Therefore, according to the results from the present study, decreasing the depth of shrimp tanks to 0.4 m increases the productivity and decreases the use of water per kilogram of shrimp produced.