The adaptability of forests during periods of environmental change depends on both tree species composition and site conditions. This study investigated whether forest health-status development (FHSD) was more dependent on tree species composition or changes in site conditions resulting from salvage cutting > 1 ha. FHSD was classified across 8526 small catchments covering the Czech Republic (78,866 km²; 115–1602 m a.s.l.) for the periods 2000–2009 and 2010–2019, based on changes in MODIS VI-derived enhanced vegetation indices (EVI) for forest soils. This was compared against the proportions of stand-forming Norway spruce (Picea abies), Scots pine (Pinus sylvestris), Common beech (Fagus sylvatica), oaks (Quercus sp.), ashes (Fraxinus sp.) and alders (Alnus sp.), as well as against elevation, temperature, precipitation and nitrogen deposition on salvage clear-cut areas, using multiple locally weighted regression (MLWR). Of the forest soil plots monitored, 81.3% were classed as having deteriorating forest status and 14.6% as sensitive, with only 2.3% classed as improving and 1.4% as resistant. While the tree species effect on FHSD increased from R² 0.00–0.67 over 2000–2009 to R² 0.09–0.76 over 2010–2019, the effect of environmental impact over the same periods increased less steeply, from R² 0.01–0.59 to R² 0.00–0.67. These increasing MLWR determination indices support the importance of tree species composition over site conditions for analyses of environmental change impacts in catchments.