The increasing threat to freshwater fish species and the resulting loss of biodiversity in freshwater systems highlight the urgent need for sustainable conservation initiatives. Human activities further exacerbate these challenges, emphasising the necessity for effective management strategies to mitigate biodiversity decline and safeguard vulnerable species. In the Irish context, freshwater systems boast a diversity of approximately 28 different fish species, with approximately 13 currently classed as native to Ireland. The relatively smaller number of native species underscores the importance of monitoring and preserving freshwater fish species from a conservation standpoint. This thesis focuses on advancing environmental DNA assays that combines Recombinase Polymerase Amplification and CRISPR-Cas technology, complemented by Lateral Flow Assay detection. These assays facilitate the specific and accurate detection of target fish species' presence or absence in Irish freshwater environments. Specifically assessing three different freshwater fish species—Esox lucius (Northern pike), Squalius cephalus (Chub), and Coregonus pollan (Pollan)—the performance of these assays is demonstrated across various conservation applications. These include monitoring a nonnative species (Northern pike), assessing the presence of an invasive species (Chub), and contributing to biodiversity management by monitoring a species under conservation (Pollan). By employing two distinct detection methods - fluorescence signal output and lateral flow visual readout - these assays successfully identify the target species using tissueextracted DNA and environmental DNA. By utilising collected environmental water samples, these assays were further validated as fit-for-purpose in field applications, establishing a robust foundation for supporting the detection and management of freshwater species. Additionally, the incorporation of Lateral Flow Assay detection enhances the performance of the developed assays, improving user-friendliness and simplifying result acquisition. This crucial feature also paves the way for future on-site adaptations. The significance of the developed assays lies in their potential to improve the efficiency of conservation efforts focused on species monitoring and management.