Since shrimp dwell and forage on the pond bed, the condition of the substrate is vital to their well-being. Pond preparation, both initially and between cycles, has a considerable impact on the substrate and water quality, particularly at the early stages of the pond production cycle. Preparation basically involves draining, drying, ploughing and chemical treatment. Drying enables air to penetrate the sediments and assists in the breakdown and mineralization of organic matter and the release of hydrogen sulphide. The mineralization of organic matter produces inorganic nutrients (nitrate, phosphate, carbonate) which will improve the fertility of the pond, reduce the oxygen demand of the sediment and so reduce the impact of any previously formed anaerobic decomposition products (Lee & Wickins, 1992).

Treating pond beds with lime has several beneficial effects. It increases the pH of the mud, improves benthic productivity, buffers against large daily fluctuations in the pH of the water, boosts primary productivity by increasing the availability of carbon dioxide for photosynthesis, and improves the availability of nutrients, particularly phosphates. Its impact is most beneficial when accompanied by a program of fertilization. Limed ponds should be filled with water and left for at least a week, and the pH of the water checked before animals are introduced. Ponds are sometimes treated with other chemicals specifically aimed at eliminating predators (Lee & Wickins, 1992).

When a pond is refilled prior to restocking, a bloom of phytoplankton can be encouraged in a little water (10-30 cm deep) by the addition of fertilizers. As the phytoplankton density increases, the water level can be raised in steps (Lee & Wickins, 1992).