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Flows of energy and matter across habitat boundaries can be major determinants of the functioning of recipient ecosystems. It is currently debated whether terrestrial dissolved organic matter (tDOM) is a resource subsidy or a resource subtraction in recipient lakes. We present data from a long-term field experiment in which pelagic phosphorus concentration and whole-ecosystem primary production increased with increasing tDOM input, suggesting that tDOM acted primarily as a direct nutrient subsidy. Piecewise structural equation modeling supports, however, a substantial contribution of a second mechanism: colored tDOM acted also as a resource subtraction by shading benthic algae, preventing them from intercepting nutrients released across the sediment-water interface. Inhibition of benthic algae by colored tDOM thus indirectly promoted pelagic algae and whole-ecosystem primary production. We conclude that cross-ecosystem terrestrial DOM inputs can modify light and nutrient flows between aquatic habitats and alter the relative contributions of benthic and pelagic habitats to total primary production. These results are particularly relevant for shallow northern lakes, which are projected to receive increased tDOM runoff.