AbstractSalvinia minima is an aquatic fern which presents several advantages for the phytoremediation of wastewater. However, there is no information available for the operation of Salvinia‐based systems (SBS) for nutrient removal from organic matter enriched wastewater. The objective of this work was to establish the optimum range of some key parameters for the operation of Salvinia minima ponds treating anaerobic effluents of coffee wastewater (AECWW). Batch cultures were performed outdoors, under subtropical conditions (Xalapa, Veracruz, Mexico). At the first stage, various pH levels were tested. After choosing the optimum pH, two pond depths were evaluated (0.10 m and 0.27 m). It was found that the productivity in AECWW was strongly affected by the pH, as it decreased with the increase in the pH. In fact, growth was completely inhibited at pH 8.0. In contrast, productivity at a pH of 6.0 and a pond depth of 0.27 m during the summer was equivalent to 27.92 ton/ha × year. The percentage of TKN removal increased with the pH value: 51 ± 2.28% at pH 5.0; 78 ± 1.47% at pH 6.0 and. 97 ± 0.80% at pH 8.0. A similar situation was found for the case of NH4‐N removal: (55 ± 0.44%, 80 ± 1.1%, 99 ± 0.02%). The depth of the culture had influence on the productivity, protein content and nutrient removal. It was concluded that Salvinia minima is an adequate choice for the treatment and recovery of nutrients from AECWW. The pH for optimal operation of this type of pond was 6.0. The depth of the water column should be adjusted to 0.10 m for attaining a maximum relative removal efficiency (in terms of g NH4‐nitrogen/l × d), although the productivity would not be at its maximum under these conditions. On the contrary, depth should be adjusted to 0.27 m for reaching the maximum absolute removal efficiency (considering the total volume of the reactor) and the maximum productivity. During the late autumn and winter period, the AECWW should be diluted 1:2 in order to enhance ammonia nitrogen removal.