The aim of this work was to test the performance of a shrimp-tomato culture system (STCS) in an arid-semiarid region (Sonora, Mexico) and to evaluate the water quality variables and phytoplankton variation of shrimp effluent and that water returning from the tomato module culture. The field study was conducted using groundwater and consisted of three circular tanks that were used for shrimp (Litopenaeus vannamei) farming and were coupled to one culture module of tomato plants (Lycopersicon esculentum). The shrimp effluent was used to irrigate the tomato plants. The yield was 11.1±0.2 kg shrimp per tank (3.9±2.0 ton ha−1) and 33.3 kg tomatoes per 45 plants (36.1±2.3 ton ha−1). During the culture, the concentrations of nutrients were (mg L−1): total N-ammonia, <0.001–0.848; N-nitrite, <0.001–1.45; N-nitrate, 5.2–172.2; dissolved reactive-P, <0.005–0.343. A total of 35 taxa belonging to three different algal classes were observed: Chlorophyta (87 to 98%), Bacilliariophyta (2 to 9%) and Cyanophyta (0–3%). This STCS allowed us to harvest the equivalent of 3.9 ton ha−1 of shrimp and 36.3 ton ha−1 of tomatoes, with a water consumption of 2.1 m3 per kg harvested of both products.