Lowland soils are commonly found in the state of Rio Grande do Sul, Southern of Brazil, where they represent around 20% of the total area of the state. Deficient drainage is the most important natural characteristic of these soils which therefore are mainly in use for flood-irrigated rice (Oriza sativa). Degradation in these soils is progressively getting stronger since the intensity of agricultural activities leads to a higher soil density, and a lower water infiltration rate. There is a growing interest by farmers to grow other crops such as soybean in rotation with rice but this degradation has become an obstacle to do so. Soil analyses have showed differences in physical, chemical and biological properties as a result of management practices adopted by farmers. This paper shows how a soil management system was chosen by farmers in relation to irrigation and drainage constraints. Parameters were considered by farmers: soil type, (expected changes in) quality of soil structure, choice of machinery, farm size, management level, labor, inputs in terms of fertilizer and pesticides, opportunities for rotation with crops other than rice. The three management system currently in use (Conventional, Semi-direct and Pre-germinated), are taken as examples. The study showed that although farmers are well aware of potentially better management systems when considering soil quality, they were often (especially the small farmers) forced to reject the choice for the best system