Aquaculture wastewater contains organics, inorganics, and microalgae, which need to be removed before being discharged into the environment or recycled. These aquaculture pollutants, especially microalgae, will reduce the membrane performance in membrane distillation (MD) process. In this work, nylon taffeta, non-woven and polyester substrates are used for microtextured surface-templating to produce superhydrophobic membranes with exciting water-repellent properties. Micro-scaled structures of different sizes are homogenously and repetitively printed on the membrane surfaces, as illustrated from FESEM and confocal micrographs. Water contact angle for all textured membranes has exceeded 150°, reflecting non-wetted and superhydrophobicity characteristics. Among them, nylon taffeta templated membrane indicates the highest advancing (155°) and receding (146°) contact angles with the lowest hysteresis of 9°. All membranes have undergone MD separation of aquaculture wastewater. Membrane printed using nylon taffeta templated demonstrated the highest flux of 30 kg/m2·h with the least deposited surface foulants. After MD separation, the organics (ammonia) and inorganics (phosphorus, calcium, sodium, magnesium, etc.) also achieved a rejection rate of at least 92%. Nylon taffeta templated membrane has shown a stable flux over 30 h DCMD separation. These findings have qualitatively explained the dynamic behavior of a membrane surface morphology on aquaculture wastewater treatment.