Invasive non-indigenous crayfish species (NICS) are a major threat to the existence of native crayfish populations in European freshwater ecosystems. The discovery of signal crayfish Pacifastacus leniusculus, marbled crayfish Procambarus virginalis, and spiny-cheek crayfish Faxonius limosus in Estonia has increased the risk of extinction of Estonia’s only native crayfish species, the noble crayfish Astacus astacus. The aim of this study was to give an overview of the status, distribution, and impacts of P. leniusculus, F. limosus, and Procambarus virginalis on A. astacus populations and assess the effect of trapping on NICS abundance. Annual monitoring of crayfish has been carried out since 2008 as part of A. astacus conservation and the NICS eradication plan. In this study, we present data from nine sampling locations monitored from 2010 to 2022. The spread of NICS continues to increase beyond their distribution areas, and in two sampling locations P. leniusculus and A. astacus live in sympatry. Our results suggest that trapping has a limited effect on population abundance, as NICS have already caused the extinction of two A. astacus populations. However, intensive trapping should continue simultaneously with sensitive molecular techniques to monitor the spread of NICS.