Environmental DNA (eDNA) is heterogeneous (e.g., tissue fragments, sloughed cells, extracellular DNA bound to particles), and there remain key knowledge gaps regarding fate and transport of eDNA in flowing waters. Seasonal changes in streams, such as allochthonous organic matter inputs during autumn leaf fall, offer both physical (via debris dams) and biological (via microbial decomposers) drivers that could increase eDNA removal from the water column. We conducted short-term additions of Common Carp (Cyprinus carpio) and Steelhead trout (Oncorhynchus mykiss) eDNA to experimental streams (50m long x 0.6m wide) lined with mixed sand/pea-gravel/cobble, fed with low-nutrient groundwater, and maintained at Q=2 L/s. We compared eDNA removal in control streams (no leaves added) to those with added leaf litter (dried sugar maple; Acer saccharum) at two standing stocks (47 vs. 23 gDM/m2) on Days 5 and 19 post-addition (N=16 releases). We quantified eDNA concentrations via droplet digital PCR, and calculated eDNA removal using declines in eDNA concentration across each reach. On Day 5, eDNA transport distances (as Sw; m) were shortest with high leaf litter (Carp Sw=23m; Steelhead Sw=42m) compared to the control stream (Carp Sw=53m; Steelhead Sw=77m). On Day 19, eDNA removal rates were only measurable with high leaves, and varied between species (Carp Sw=16m; Steelhead Sw=109m). There was no eDNA removal in the control stream, perhaps confounded by significantly colder water temperatures (Day 5=16°C vs. Day 19=10°C). When converted to depositional velocity (Vdep; mm/sec), Carp eDNA Vdep with high leaves was 3x higher (0.16 mm/sec) than for Steelhead (Vdep=0.05 mm/sec), and 2x higher than Carp Vdep measured previously during summer (Vdep= 0.08 mm/sec). Our results show that both species and environmental context matters; in order to effectively use eDNA as a conservation tool for species of concern in streams/rivers, we must identify controls on eDNA removal from the water column.