The European Sardine and the Atlantic Horse Mackerel are small pelagic fish that occur in the Southern Alboran Sea (Moroccan coast) and have an important socio-economic value. The world’s fisheries terrible condition, with overfishing and environmental degradation pushing stock to unsustainable levels. While sustainable management is paramount, traditional single species approaches are insufficient. Ecosystem models have emerged as powerful tools to understand the complex interaction between fish populations, their environment, and human activities. The Moroccan main ports landing logbook from 2009 to 2022, climate scenario variables: RCP 8.5 were used in this paper. The Generalized Additive Models (GAMs) (a Machine-Learning Approach) were used to analyze the relationships between LPUE, Effort, and various environmental factors for both species. This paper investigates the influence of climate scenario on the Landing per Unit Effort (LPUE) and Effort to develop future potential landings for both species. It also compares the proportion change to the 2010–2022 average in the Southern Alboran Sea between 2022 and 2100. Phytoplankton and Sea Surface Temperature were identified as the main drivers of the Sardine LPUE. Moreover, the Sea Level Anomaly and Sea Surface Temperature influenced the Horse Mackerel LPUE. The Sardine potential landing increases by the end of the 21st century by + 5%. Furthermore, the Atlantic Horse Mackerel potential landings are projected to decrease by −100% significantly under RCP 8.5 compared to the 2010–2022 average by the end of the 21st century. This paper highlights the importance of considering environmental factors in managing small pelagic fisheries and emphasizes the need for adaptive management strategies and conservation measures to ensure their sustainability under a changing climate.