Wetland ecosystems in Africa's semi-arid rift valleys are crucial for supporting biodiversity, regulating water systems, and sustaining livelihoods; however, they are rapidly deteriorating due to agricultural expansion and urbanization. Previous assessments have often relied on global valuation coefficients and moderate-accuracy models, limiting their relevance for local restoration planning. This study introduces an integrated framework that combines high-accuracy Random Forest land cover classification, machine learning-enhanced CA-Markov modeling, spatial water quality assessment, and locally calibrated ecosystem service valuation to quantify changes in land cover, water quality degradation, and trends in ecosystem service value (ESV) within Ethiopia's Ziway-Shalla Sub-Basin from 1995 to 2025, with projections extending to 2045. Over the past 30 years, farmland has expanded from 59.0% to 75.2%, while forest cover has drastically declined from 20.9% to just 1.4%. Consistently, water quality has exceeded environmental thresholds (with electrical conductivity at 1880 mu S/cm, nitrate at 48.3 mg/L, and phosphate at 5.4 mg/L), leading to hypereutrophic conditions. Overall, the total ESV has decreased by 19.4%, with forest and wetland services diminishing by 97.7% and 51.6%, respectively, while provisioning services have increased by 29.2%, and regulating and supporting services have declined by 18.2% and 57.2%, respectively. Projections indicate that by 2045, forest cover may decrease further to 0.3%, with barren land doubling. A multi-criteria restoration analysis has prioritized 38% of the basin for intervention, identifying 5.6% as emergency hotspots. A phased restoration strategy that emphasizes the protection of critical areas, along with agroforestry/conservation agriculture and Payments for Ecosystem Services, presents a scalable model for semi-arid landscapes worldwide, directly contributing to the achievement of SDGs 1, 2, 6, 13, 15, and 17. This framework provides robust and actionable insights for targeted conservation efforts and sustainable land management in rapidly changing rift valley landscapes.