The practices (tillage and flooding) used for rice crops are unsustainable, especially in areas characterized by water shortages, such as the Mediterranean region. Therefore, it is necessary to develop sustainable methods in order to ensure the viability of rice production. However, it is essential to understand the effects that alternative management can have on herbicide behavior. In this context, this paper describes the first field experiment conducted to evaluate the medium-term effects of different agricultural practices on the fate of bispyribac sodium (BPS). Thus, the treatments were as follows: tillage and flooding (TF), tillage and sprinkler (TS), and no-tillage and sprinkler (NTS). In addition, “alperujo” compost (AC) from olive mill waste was used in each treatment (TF-AC, TS-AC, and NTS-AC). The AC was applied only once in 2015 when the TS and NTS treatments were implemented. The AC amendment increased the adsorption of BPS and its irreversibility, thereby decreasing the BPS leaching capacity. Furthermore, throughout this study, the BPS persistence was up to 1.85 times greater with sprinklers than in the flooding condition, which could explain the high values of BPS effectiveness (increased by a factor of 1.45 on average) found with sprinklers. Therefore, the implementation of sprinklers in combination with AC can be considered a sustainable strategy for Mediterranean rice production, at least in the medium term, as it reduces BPS water pollution and increases its weed control efficiency.