We analysed the effectiveness of agricultural best management practices (BMPs) for mitigating harmful algal blooms (HABs) in the Mar Menor lagoon, Spain, by coupling SWAT + catchment and GOTM-WET lake models. We compared the effectiveness of different BMP scenarios, including “vegetative filter strips”, “contour farming”, “fertilizer reduction”, “crop rotation”, and their combination for reducing high chlorophyll a (Chl-a) events over the period 2003–2022. All BMPs significantly reduced nutrient inputs entering the lagoon, which limited the formation of HABs. The scenario that combined all BMPs was the most effective in controlling HABs, decreasing the numbers of days with HABs by 81 %, and the Chl-a by 50 % during periods of HABs. This was mainly explained by the effectiveness of crop rotation, fertilizer reduction and vegetative filter strips in differentially reducing nutrient inputs (e.g. crop rotation reduced nitrogen by 47.4 % and phosphorus by 31.8 %). Contour farming was the least effective BMP in reducing nutrient inputs, and thus controlling HABs (1.6 % in Chl-a reduction and 5.8 % in days with HAB). The results suggest that HABs dynamics in Mar Menor are controlled by interactive effects of different nutrient forms, where orthophosphate plays a key role in initiating the HABs which is then maintained by high nitrogen concentrations. This research underscores the relevance of agricultural BMPs for effectively mitigating HABs driven by eutrophication in coastal vulnerable aquatic ecosystems like Mar Menor. Coupling SWAT+ and GOTM-WET models, moved beyond solely nutrient simulations and allowed the incorporation of lagoon responses to BMPs for HAB prevention.