Environmental DNA (eDNA) has emerged as a non-invasive tool for monitoring aquatic ecosystems, allowing researchers to efficiently detect invasive species, assess biodiversity, track organismal activity, and identify rare species without disturbing the environment. Manual methods for collecting eDNA are time-consuming, labor-intensive, and limit spatial and temporal coverage. Autonomous systems have been developed to address the limitations of manual eDNA collection. However, many current platforms are costly, large, offer limited sample throughput, and face challenges with maintaining eDNA integrity during collection, storage, and transport. The goal of this study is to design a modular, scalable, and reliable eDNA sampling system that is capable of autonomously filtering and preserving discrete eDNA samples in situ. The main components of this system include a peristaltic pump, 2-way normally- closed solenoids, a custom manifold for fluid handling, an ESP32 microcontroller, and industry-standard 0.22 μm Sterivex filters. The prototype under development is designed for high-throughput with onboard capacity of 36 discrete filters and will maintain DNA integrity by automating post-filtration preservation. Following validation, the design will be scaled to maximize filter capacity and expand field operations. Remote configuration of sampling frequency is supported through the ESP32 microcontroller and will enhance the flexibility of the system. This proposed system offers a solution to challenges and limitations in manual and autonomous sampling by reducing labor intensity and time demands while maintaining sample integrity and offering a cost-effective alternative.