Fungi play a crucial role in the breakdown of aquatic leaf litter, yet their life histories are not well understood. Although many aquatic fungi spend their whole life cycle in the river, a suite of studies suggest that some aquatic fungi have a terrestrial life stage and enter the water with the leaf1,2. Amplicon sequencing has revealed far greater fungal richness on submersed litter than morphological studies or culturing. Amplicon sequencing, however, cannot differentiate whether taxa are growing or dormant. We used quantitative stable isotope probing (qSIP), of the ITS region, to identify which fungal taxa were growing and their growth rates on two leaf types (Sycamore and Cottonwood) that were submerged in Beaver Creek, Arizona for 29 days. We also sequenced fungi on senesced leaves prior to submersion. This is the first in-stream study using qSIP to study fungi during decomposition. We found that only 25% of fungal taxa on the submerged leaves were growing, however these taxa accounted for 42-52% of the relative abundance. Additionally, 15-30% of fungal taxa growing on the submersed leaves came in with the leaves. These treetop fungi accounted for 65-76% of the relative abundance of growing fungi. This research demonstrates that some treetop fungi play a role in aquatic leaf litter decomposition. Fungal life histories, like the life histories of insects and amphibians, can extend from the tops of trees to the bottoms of rivers.