Land use carries implications for freshwater fish conservation. Plantation forestry practices have been shown to have negative impacts on resident fish fauna, but little work has been conducted to assess these impacts on invasive vs. native fish populations. Ten headwater catchments in the Mediterranean climate zone of Chile were used to assess the impacts of land use (pine plantations vs. native forests) on fish condition (length-weight relationship) and abundance (catch-per-unit-effort (CPUE)) of the invasive trout Oncorhynchus mykiss and the threatened native catfish Nematogenys inermis. Negative impacts on trout condition were associated with a lack of canopy cover and river topology. The presence of N. inermis was associated with catchment factors less favourable to trout. Current environmental regulations and forestry management practices do not appear to create negative pressures on invasive trout from land use practices, despite expectations from the literature. Assessing how land use management regulations impact invasive and native fishes should be a part of species conservation and territorial planning.