Ecological biodiversity is declining at an unprecedented rate. To combat such irreversible changes in natural ecosystems, biodiversity conservation initiatives are being conducted globally. However, the lack of a feasible methodology to quantify biodiversity in real-time and investigate population dynamics in spatiotemporal scales, prevents the use of ecological data in environmental planning. Traditionally, ecological studies rely on the census of an animal population by the “capture, mark and recapture” technique. In this technique, human field workers manually count, tag, and observe tagged individuals, making it time-consuming, expensive, and cumbersome to patrol the entire area. Recent research has also demonstrated the potential for inexpensive and accessible sensors for ecological data monitoring. However, stationary sensors collect localized data, which is highly specific on the placement of the setup. In this research, we propose the methodology for biodiversity monitoring using state-of-the-art deep learning (DL) methods operating in real-time on sample payloads of mobile robots. Such trained DL algorithms demonstrate a mean average precision (mAP) of 90.51% in an average inference time of 67.62 milliseconds within 6,000 training epochs. We claim that using such mobile platform setups inferring real-time ecological data can help us achieve our goal of quick and effective biodiversity surveys. An experimental test payload is fabricated, and online as well as offline field surveys are conducted, validating the proposed methodology for species identification that can be further extended to geo-localisation of flora and fauna in any ecosystem.