1 Supporting Information 2 Table S1. List, data scale and description of the biological traits considered in this study. All 3 information was obtained from the Fish Traits database (Frimpong & Angermeier, 2009). Body size, reproductive ecology, and life history traits Salinity traits Trophic ecology traits Trait type Field code Data scale Description benthic binary Benthic feeder surwcol binary Surface or water column feeder algphyto binary Algae or phytoplankton, including filamentous algae macvascu binary Any part of macrophytes and vascular plants detritus binary Detritus or unidentifiable vegetative matter invlvfsh binary Aquatic and terrestrial invertebrates fshcrcrb binary Larger fishes, crayfishes, crabs, frogs, etc. eggs binary Eggs of fishes, frogs, etc. maxtl continuous Maximum total length (centimeters) Mean, median, or modal age at maturity for females matuage continuous (years) longevity continuous Longevity (years) fecundity count Maximum reported fecundity serial binary Serial or batch spawner season euryhaline continuous Approximate length of the spawning season (months) binary Species with wide salinity tolerance 4 1 Habitat preference traits muck binary Muck substrate claysilt binary Clay or silt substrate sand binary Sand substrate gravel binary Gravel substrate cobble binary Cobble or pebble substrate boulder binary Boulder substrate bedrock binary Bedrock substrate vegetat binary Aquatic vegetation debrdetr binary Organic debris or detrital substrate lwd binary Large woody debris preflot binary Lotic and lentic systems but more often in lotic preflen binary Lotic and lentic systems but more often in lentic largeriv binary Medium to large river smallriv binary Stream to small river creek binary Creek sprgsubt binary Spring or subterranean water lacustrine binary Lentic systems lowland binary Lowland elevation upland binary Highland elevation montane binary Mountainous physiography slowcurr binary Slow current modcurr binary Moderate current fastcurr binary Fast current 2 5 Figure S1. Long-term trajectories (1994-2008) of total native and non-native fish abundance 6 (count data, log10(X+1) transformed) across the seven monitoring sites and globally. The dotted 7 line at Bear Siding site in 2004 indicates no sampling due to high turbidity. 8 9 3 10 Figure S2. Comparison of the discharge anomaly effects estimated by the two species models 11 that received highest support (model 5, AICc = 1104.2; model 6, AICc = 1104.6; see Table 1). In 12 both models observation error was species-specific. Whereas in model 5 biotic interactions were 13 allowed, in model 6 they were not allowed (see Table 1). 14 4 15 Figure S3. Results of the Beta diversity partitioning. The relative contributions of the nestedness 16 (βNES) and the turnover (βSIM) components to overall beta diversity (βSOR) across the studied 17 period 1994 – 2008 are shown. 18 19 5 20 References 21 Frimpong, E. A., & Angermeier, P. L. (2009). Fish traits: a database of ecological and life- 22 history traits of freshwater fishes of the United States. Fisheries, 34(10), 487–495. 23 6