Many dryland areas are being converted into intensively managed irrigation crops, what can disrupt the hydrological regime, degrade soil and water quality, enhance siltation, erosion and bank instability, and affect biological communities. Still, the impacts of irrigation schemes on the functioning of terrestrial and aquatic ecosystems are poorly understood. Here we assess the effects of irrigation agriculture on breakdown of coarse organic matter in soil and water. We measured breakdown rates of alder and holm oak leaves, and of poplar sticks in terrestrial and aquatic sites following a gradient of increasing irrigation agriculture in a semi-arid Mediterranean basin transformed into irrigation agriculture in 50% of its surface. Spatial patterns of stick breakdown paralleled those of leaf breakdown. In soil, stick breakdown rates were extremely low in non-irrigated sites (0.0001-0.0003 day(-1)), and increased with the intensity of agriculture (0.0018-0.0044 day(-1)). In water, stick breakdown rates ranged from 0.0005 to 0.001 day(-1), and increased with the area of the basin subject to irrigation agriculture. Results showed that irrigation agriculture affects functioning of both terrestrial and aquatic ecosystems, accelerating decomposition of organic matter, especially in soil. These changes can have important consequences for global carbon budgets.