We developed a recirculating system integrating shrimp culture with microbial mats aiming to mitigate the environmental impacts of by-products from shrimp culture and to advance toward the bioremediation of the shrimp culture water. The microbial consortia collected from natural environments (TaM) was constituted by bacteria (55.6%), Cyanophyte (18.4%), diatoms (9%), nematods (5.6%) and Chlorophyte algae (1.4%) among the major taxonomic groups. The removal of nutrients and solids by these mats was assessed in a recirculating system (2 cycles/hour) (n = 3) containing 60 and 120 ind m-2 of Litopenaeus vannamei. Results showed that the microbial mat reduces daily up to 71% of ammonia nitrogen, decreases around 68% of the biochemical oxygen demand (DBO5) and up to 62% of suspended solids (SST) when comparing to the control systems (p < 0.05). By trapping organic and mineral matter, microbial mats have a clarifying effect on the water column. The mats effectively traps particulate matter and break it down with great efficiency due to the tight coupling between autotrophs and nitrifyers in the mat. This feature increases inorganic nitrogen levels in water column and accelerates nitrification up to 10 mg N-NO3 - L-1 (120 ind m-2) producing 750% more nitrates than the control systems. Nevertheless, phosphorus removal was not significant (p > 0.05). The Bioremediated culture water had a positive effect on the culture of Litopenaeus vannamei, and promotes higher survival and growth in presence of TaM in the recirculating shrimp culture system.