Deforestation, environmental pollution, and the overexploitation of resources, in addition to the Earth's natural cycles, are scaling up the impacts of climate change in the provision of Ecosystem Services (ES). Green-Blue Ecosystems (GBE) are impacted by climatic conditions, topography, and water presence. Data-driven modelling techniques may effectively capture the effects of seasonal variations while modelling natural ecosystems. This research proposes a hybrid modelling approach that combines Deep Learning and traditional Machine Learning, Sensitivity Analysis and Feature Importance Evaluation (FIE) to investigate seasonality effects on mapping GBE. The models, built using satellite imagery from the Spring and Summer seasons of the Mediterranean climate zone, included spectral indices, topography (DEM), and groundwater depth (GD). The model that best suited the analysis was selected using sensitivity tests and hyperparameter optimization. The study shows that land cover classes of transitional woodland shrubs, inland marshes, cultivated land parcels, and watercourses are better classified in the Spring, with an accuracy of 0.814. FIE indicates that spectral indices are the most important predictors for detecting green ecosystems in both seasons. Additionally, DEM and GD are the most relevant predictors to classify watercourses in the Summer. An analytical examination of the input data and hyperparameter settings facilitates understanding of models' behaviour while improving models' prediction. This research provides an advanced understanding of the effects of seasonal variations on the status of GBE and enhances understanding of modelling ES in areas with a growing need for changes in land use and high water supply demand.