Best management practices (BMPs) provide a feasible solution for non-point source pollution problems. High sediment and nutrient yields without retention control result in environmental deterioration of surrounding areas. In the present study, the soil and water assessment tool (SWAT) model was developed for El Beal watershed, an anthropogenic and ungauged basin located in the southeast of Spain that drains into a coastal lagoon of high environmental value. The effectiveness of five BMPs (contour planting, filter strips, reforestation, fertilizer application and check dam restoration) was quantified, both individually and in combination, to test their impact on sediment and nutrient reduction. For calibration and validation processes, actual evapotranspiration (AET) data obtained from a remote sensing dataset called Global Land Evaporation Amsterdam Model (GLEAM) were used. The SWAT model achieved good performance in the calibration period, with statistical values of 0.78 for Kling–Gupta efficiency (KGE), 0.81 for coefficient of determination (R2), 0.58 for Nash–Sutcliffe efficiency (NSE) and 3.9% for percent bias (PBIAS), as well as in the validation period (KGE = 0.67, R2 = 0.83, NS = 0.53 and PBIAS = −25.3%). The results show that check dam restoration is the most effective BMP with a reduction of 90% in sediment yield (S), 15% in total nitrogen (TN) and 22% in total phosphorus (TP) at the watershed scale, followed by reforestation (S = 27%, TN = 16% and TP = 20%). All effectiveness values improved when BMPs were assessed in combination. The outcome of this study could provide guidance for decision makers in developing possible solutions for environmental problems in a coastal lagoon.